HEADER CELL ADHESION 21-JAN-09 2W94
TITLE NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT
TITLE 2 1.8 ANGSTROM RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DISCOIDIN-1 SUBUNIT A;
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: DISCOIDIN I, DISCOIDIN-1 SUBUNIT ALPHA, DISCOIDIN I CHAIN A;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM;
SOURCE 3 ORGANISM_COMMON: SLIME MOLD;
SOURCE 4 ORGANISM_TAXID: 366501;
SOURCE 5 STRAIN: AX2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB
KEYWDS CELL ADHESION, H TYPE LECTIN
EXPDTA X-RAY DIFFRACTION
AUTHOR K.SABOIA ARAGAO,A.IMBERTY,A.VARROT
REVDAT 5 13-DEC-23 2W94 1 REMARK LINK
REVDAT 4 21-JUL-10 2W94 1 JRNL REMARK
REVDAT 3 07-JUL-10 2W94 1 JRNL
REVDAT 2 26-MAY-10 2W94 1 JRNL FORMUL
REVDAT 1 31-MAR-10 2W94 0
JRNL AUTH S.MATHIEU,K.SABOIA ARAGAO,A.IMBERTY,A.VARROT
JRNL TITL DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AND INTERACTIONS
JRNL TITL 2 WITH OLIGOSACCHARIDES: SPECIFICITY, AFFINITY, CRYSTAL
JRNL TITL 3 STRUCTURES AND COMPARISON WITH DISCOIDIN II.
JRNL REF J.MOL.BIOL. V. 400 540 2010
JRNL REFN ISSN 0022-2836
JRNL PMID 20580724
JRNL DOI 10.1016/J.JMB.2010.05.042
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0066
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6
REMARK 3 NUMBER OF REFLECTIONS : 71665
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.167
REMARK 3 R VALUE (WORKING SET) : 0.165
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3802
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4683
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2260
REMARK 3 BIN FREE R VALUE SET COUNT : 245
REMARK 3 BIN FREE R VALUE : 0.2880
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5975
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 64
REMARK 3 SOLVENT ATOMS : 981
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.81
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.31000
REMARK 3 B22 (A**2) : -2.32000
REMARK 3 B33 (A**2) : 1.01000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.123
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.447
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6158 ; 0.017 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 5323 ; 0.000 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8406 ; 1.496 ; 1.920
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12323 ; 0.695 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 757 ; 7.365 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;35.000 ;24.272
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 933 ;11.892 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.859 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 945 ; 0.100 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6967 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1309 ; 0.000 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3773 ; 0.839 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6124 ; 1.379 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2385 ; 2.190 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2282 ; 3.171 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
REMARK 4
REMARK 4 2W94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-09.
REMARK 100 THE DEPOSITION ID IS D_1290038601.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-JUN-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.933
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29532
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 28.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 0.23000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2VM9
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M LISO4 100 MM HEPES 7.5, PH 7.5
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.96400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.96400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.26500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 137.18550
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.26500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 137.18550
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.96400
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.26500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 137.18550
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.96400
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.26500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 137.18550
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 15010 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.2 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH B2038 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B2039 LIES ON A SPECIAL POSITION.
REMARK 375 HOH C2081 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 ALA B 0
REMARK 465 ALA C 0
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OG SER B 156 O HOH B 2232 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASN A 38 -161.57 -128.12
REMARK 500 ALA A 49 159.40 169.14
REMARK 500 THR A 211 53.34 37.21
REMARK 500 ASN A 236 -141.51 50.99
REMARK 500 ASN B 24 -167.09 -160.74
REMARK 500 ASN B 38 -164.02 -121.60
REMARK 500 ALA B 49 158.81 176.34
REMARK 500 VAL B 98 -58.05 -125.41
REMARK 500 ASP B 164 42.75 70.07
REMARK 500 ASN B 236 -142.49 58.00
REMARK 500 ASN C 38 -163.58 -125.40
REMARK 500 ALA C 49 158.76 169.33
REMARK 500 ASN C 236 -142.73 55.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH B2049 DISTANCE = 6.27 ANGSTROMS
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 2-METHYL-2,4-PENTANEDIOL (MPD): CYOPROTECTANT
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A1258 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 16 ND1
REMARK 620 2 HIS B 16 ND1 108.6
REMARK 620 3 HIS C 16 ND1 110.9 112.3
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1257 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 164 OD1
REMARK 620 2 ASP A 203 OD2 87.4
REMARK 620 3 ASP A 246 OD2 128.3 98.9
REMARK 620 4 ASP A 246 OD1 78.5 92.6 50.2
REMARK 620 5 GLN B 219 OE1 81.2 85.3 150.2 159.6
REMARK 620 6 HOH B2281 O 90.4 176.0 85.1 90.3 91.0
REMARK 620 7 HOH B2282 O 153.5 80.9 77.2 125.4 74.3 99.7
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA C1257 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLN A 219 OE1
REMARK 620 2 HOH A2288 O 91.4
REMARK 620 3 HOH A2289 O 75.1 97.5
REMARK 620 4 ASP C 164 OD1 83.5 92.6 156.4
REMARK 620 5 ASP C 203 OD2 88.8 179.4 82.0 87.9
REMARK 620 6 ASP C 246 OD2 147.3 81.6 74.2 128.5 97.9
REMARK 620 7 ASP C 246 OD1 163.6 91.1 120.6 80.2 88.8 49.1
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B1256 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 164 OD1
REMARK 620 2 ASP B 203 OD2 88.7
REMARK 620 3 ASP B 246 OD2 128.3 97.3
REMARK 620 4 ASP B 246 OD1 78.7 87.9 50.5
REMARK 620 5 GLN C 219 OE1 81.5 88.7 149.5 160.0
REMARK 620 6 HOH C2263 O 94.0 175.7 83.5 95.8 88.5
REMARK 620 7 HOH C2264 O 157.0 82.1 74.1 121.8 77.2 94.2
REMARK 620 N 1 2 3 4 5 6
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1254
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1255
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1256
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1257
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1258
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1259
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1254
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1255
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1256
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD C 1254
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD C 1255
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1256
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 1257
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2W95 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN
REMARK 900 COMPLEX WITH GALNAC AT 1.75 ANGSTROM RESOLUTION
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 FIRST RESIDUE IS ADDED FOLLOWING THE CLEAVAGE OF THE
REMARK 999 N TERMINAL HIS TAG
DBREF 2W94 A 0 0 PDB 2W94 2W94 0 0
DBREF 2W94 A 1 253 UNP P02886 DIS1A_DICDI 1 253
DBREF 2W94 B 0 0 PDB 2W94 2W94 0 0
DBREF 2W94 B 1 253 UNP P02886 DIS1A_DICDI 1 253
DBREF 2W94 C 0 0 PDB 2W94 2W94 0 0
DBREF 2W94 C 1 253 UNP P02886 DIS1A_DICDI 1 253
SEQRES 1 A 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN
SEQRES 2 A 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY
SEQRES 3 A 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN
SEQRES 4 A 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS
SEQRES 5 A 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY
SEQRES 6 A 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN
SEQRES 7 A 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS
SEQRES 8 A 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR
SEQRES 9 A 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN
SEQRES 10 A 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA
SEQRES 11 A 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS
SEQRES 12 A 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN
SEQRES 13 A 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY
SEQRES 14 A 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU
SEQRES 15 A 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR
SEQRES 16 A 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS
SEQRES 17 A 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO
SEQRES 18 A 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR
SEQRES 19 A 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP
SEQRES 20 A 254 TYR ILE ALA THR ALA LEU GLU
SEQRES 1 B 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN
SEQRES 2 B 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY
SEQRES 3 B 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN
SEQRES 4 B 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS
SEQRES 5 B 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY
SEQRES 6 B 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN
SEQRES 7 B 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS
SEQRES 8 B 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR
SEQRES 9 B 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN
SEQRES 10 B 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA
SEQRES 11 B 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS
SEQRES 12 B 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN
SEQRES 13 B 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY
SEQRES 14 B 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU
SEQRES 15 B 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR
SEQRES 16 B 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS
SEQRES 17 B 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO
SEQRES 18 B 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR
SEQRES 19 B 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP
SEQRES 20 B 254 TYR ILE ALA THR ALA LEU GLU
SEQRES 1 C 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN
SEQRES 2 C 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY
SEQRES 3 C 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN
SEQRES 4 C 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS
SEQRES 5 C 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY
SEQRES 6 C 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN
SEQRES 7 C 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS
SEQRES 8 C 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR
SEQRES 9 C 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN
SEQRES 10 C 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA
SEQRES 11 C 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS
SEQRES 12 C 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN
SEQRES 13 C 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY
SEQRES 14 C 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU
SEQRES 15 C 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR
SEQRES 16 C 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS
SEQRES 17 C 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO
SEQRES 18 C 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR
SEQRES 19 C 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP
SEQRES 20 C 254 TYR ILE ALA THR ALA LEU GLU
HET MPD A1254 8
HET MPD A1255 8
HET SO4 A1256 5
HET CA A1257 1
HET NI A1258 1
HET SO4 A1259 5
HET MPD B1254 8
HET SO4 B1255 5
HET CA B1256 1
HET MRD C1254 8
HET MRD C1255 8
HET SO4 C1256 5
HET CA C1257 1
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
HETNAM SO4 SULFATE ION
HETNAM CA CALCIUM ION
HETNAM NI NICKEL (II) ION
HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL
FORMUL 4 MPD 3(C6 H14 O2)
FORMUL 6 SO4 4(O4 S 2-)
FORMUL 7 CA 3(CA 2+)
FORMUL 8 NI NI 2+
FORMUL 13 MRD 2(C6 H14 O2)
FORMUL 17 HOH *981(H2 O)
HELIX 1 1 LEU A 9 ASN A 12 1 4
HELIX 2 1 LEU B 9 ASN B 12 1 4
HELIX 3 1 LEU C 9 ASN C 12 1 4
SHEET 1 AA 6 HIS A 16 THR A 19 0
SHEET 2 AA 6 ILE A 61 CYS A 65 -1 O VAL A 62 N ARG A 18
SHEET 3 AA 6 ILE A 127 ASN A 140 -1 O ILE A 132 N ALA A 63
SHEET 4 AA 6 TRP A 85 SER A 94 0
SHEET 5 AA 6 TRP A 100 TYR A 103 -1 O PHE A 101 N TYR A 93
SHEET 6 AA 6 VAL A 109 GLY A 111 -1 O VAL A 109 N TYR A 89
SHEET 1 AB 3 VAL A 119 PHE A 122 0
SHEET 2 AB 3 ARG A 69 GLN A 77 0
SHEET 3 AB 3 SER A 144 THR A 151 0
SHEET 1 AC 3 SER A 157 TYR A 166 0
SHEET 2 AC 3 VAL A 240 LEU A 252 -1 O ALA A 245 N ILE A 165
SHEET 3 AC 3 LYS A 197 THR A 208 -1 O LYS A 197 N THR A 250
SHEET 1 AD 3 ARG A 180 LYS A 187 0
SHEET 2 AD 3 GLY A 227 THR A 234 -1 O PHE A 228 N VAL A 186
SHEET 3 AD 3 GLY A 217 ARG A 221 -1 O GLY A 217 N TYR A 233
SHEET 1 BA 6 HIS B 16 THR B 19 0
SHEET 2 BA 6 ILE B 61 CYS B 65 -1 O VAL B 62 N ARG B 18
SHEET 3 BA 6 ILE B 127 ASN B 140 -1 O ILE B 132 N ALA B 63
SHEET 4 BA 6 TRP B 85 SER B 94 0
SHEET 5 BA 6 TRP B 100 TYR B 103 -1 O PHE B 101 N TYR B 93
SHEET 6 BA 6 VAL B 109 GLY B 111 -1 O VAL B 109 N TYR B 89
SHEET 1 BB 3 VAL B 119 PHE B 122 0
SHEET 2 BB 3 ARG B 69 GLN B 77 0
SHEET 3 BB 3 SER B 144 THR B 151 0
SHEET 1 BC 3 SER B 157 TYR B 166 0
SHEET 2 BC 3 VAL B 240 LEU B 252 -1 O ALA B 245 N ILE B 165
SHEET 3 BC 3 LYS B 197 THR B 208 -1 O LYS B 197 N THR B 250
SHEET 1 BD 3 ARG B 180 LYS B 187 0
SHEET 2 BD 3 GLY B 227 THR B 234 -1 O PHE B 228 N VAL B 186
SHEET 3 BD 3 GLY B 217 ARG B 221 -1 O GLY B 217 N TYR B 233
SHEET 1 CA 6 HIS C 16 THR C 19 0
SHEET 2 CA 6 ILE C 61 CYS C 65 -1 O VAL C 62 N ARG C 18
SHEET 3 CA 6 ILE C 127 ASN C 140 -1 O ILE C 132 N ALA C 63
SHEET 4 CA 6 TRP C 85 SER C 94 0
SHEET 5 CA 6 TRP C 100 TYR C 103 -1 O PHE C 101 N TYR C 93
SHEET 6 CA 6 VAL C 109 GLY C 111 -1 O VAL C 109 N TYR C 89
SHEET 1 CB 3 VAL C 119 PHE C 122 0
SHEET 2 CB 3 ARG C 69 GLN C 77 0
SHEET 3 CB 3 SER C 144 THR C 151 0
SHEET 1 CC 3 SER C 157 TYR C 166 0
SHEET 2 CC 3 VAL C 240 LEU C 252 -1 O ALA C 245 N ILE C 165
SHEET 3 CC 3 LYS C 197 THR C 208 -1 O LYS C 197 N THR C 250
SHEET 1 CD 3 ARG C 180 LYS C 187 0
SHEET 2 CD 3 GLY C 227 THR C 234 -1 O PHE C 228 N VAL C 186
SHEET 3 CD 3 GLY C 217 ARG C 221 -1 O GLY C 217 N TYR C 233
LINK ND1 HIS A 16 NI NI A1258 1555 1555 2.51
LINK OD1 ASP A 164 CA CA A1257 1555 1555 2.30
LINK OD2 ASP A 203 CA CA A1257 1555 1555 2.40
LINK OE1 GLN A 219 CA CA C1257 1555 1555 2.38
LINK OD2 ASP A 246 CA CA A1257 1555 1555 2.58
LINK OD1 ASP A 246 CA CA A1257 1555 1555 2.49
LINK CA CA A1257 OE1 GLN B 219 1555 1555 2.41
LINK CA CA A1257 O HOH B2281 1555 1555 2.37
LINK CA CA A1257 O HOH B2282 1555 1555 2.41
LINK NI NI A1258 ND1 HIS B 16 1555 1555 2.28
LINK NI NI A1258 ND1 HIS C 16 1555 1555 2.35
LINK O HOH A2288 CA CA C1257 1555 1555 2.36
LINK O HOH A2289 CA CA C1257 1555 1555 2.50
LINK OD1 ASP B 164 CA CA B1256 1555 1555 2.39
LINK OD2 ASP B 203 CA CA B1256 1555 1555 2.41
LINK OD2 ASP B 246 CA CA B1256 1555 1555 2.57
LINK OD1 ASP B 246 CA CA B1256 1555 1555 2.53
LINK CA CA B1256 OE1 GLN C 219 1555 1555 2.44
LINK CA CA B1256 O HOH C2263 1555 1555 2.38
LINK CA CA B1256 O HOH C2264 1555 1555 2.44
LINK OD1 ASP C 164 CA CA C1257 1555 1555 2.38
LINK OD2 ASP C 203 CA CA C1257 1555 1555 2.39
LINK OD2 ASP C 246 CA CA C1257 1555 1555 2.70
LINK OD1 ASP C 246 CA CA C1257 1555 1555 2.56
SITE 1 AC1 6 VAL A 62 ARG A 92 TRP A 100 HOH A2345
SITE 2 AC1 6 HOH A2346 ASN C 12
SITE 1 AC2 6 ARG A 79 GLN A 84 HIS A 142 HOH A2047
SITE 2 AC2 6 THR B 41 HOH B2075
SITE 1 AC3 5 ARG A 104 VAL A 109 THR A 110 HIS A 121
SITE 2 AC3 5 HOH A2347
SITE 1 AC4 6 ASP A 164 ASP A 203 ASP A 246 GLN B 219
SITE 2 AC4 6 HOH B2281 HOH B2282
SITE 1 AC5 4 HIS A 16 HIS B 16 HIS C 16 HOH C2035
SITE 1 AC6 7 SER A 157 VAL A 158 THR A 159 SER B 157
SITE 2 AC6 7 THR B 159 SER C 157 THR C 159
SITE 1 AC7 6 THR A 41 TYR B 23 ARG B 79 GLN B 84
SITE 2 AC7 6 HIS B 142 HOH B2042
SITE 1 AC8 4 ARG B 104 VAL B 109 THR B 110 HIS B 121
SITE 1 AC9 6 ASP B 164 ASP B 203 ASP B 246 GLN C 219
SITE 2 AC9 6 HOH C2263 HOH C2264
SITE 1 BC1 6 ARG C 18 VAL C 62 ARG C 92 TRP C 100
SITE 2 BC1 6 HIS C 135 HOH C2305
SITE 1 BC2 6 THR C 41 ASN C 42 ARG C 79 GLN C 84
SITE 2 BC2 6 HIS C 142 HOH C2075
SITE 1 BC3 6 ARG C 104 VAL C 109 THR C 110 HIS C 121
SITE 2 BC3 6 HOH C2165 HOH C2306
SITE 1 BC4 6 GLN A 219 HOH A2288 HOH A2289 ASP C 164
SITE 2 BC4 6 ASP C 203 ASP C 246
CRYST1 72.530 274.371 85.928 90.00 90.00 90.00 C 2 2 21 24
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013787 0.000000 0.000000 0.00000
SCALE2 0.000000 0.003645 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011638 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
