HEADER SUGAR BINDING PROTEIN 13-AUG-08 2ZQO
TITLE CRYSTAL STRUCTURE OF THE EARTHWORM R-TYPE LECTIN C-HALF IN COMPLEX
TITLE 2 WITH GALNAC
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 29-KDA GALACTOSE-BINDING LECTIN;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: LUMBRICUS TERRESTRIS;
SOURCE 3 ORGANISM_COMMON: COMMON EARTHWORM;
SOURCE 4 ORGANISM_TAXID: 6398;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21
KEYWDS EARTHWORM LUMBRICUS TERRESTRIS, HEMAGGLUTININ, R-TYPE LECTIN, BETA-
KEYWDS 2 TREFOIL FOLD, SUGAR COMPLEX, LECTIN, SUGAR BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR R.SUZUKI,A.KUNO,T.HASEGAWA,J.HIRABAYASHI,K.KASAI,M.MOMMA,Z.FUJIMOTO
REVDAT 4 01-NOV-23 2ZQO 1 HETSYN
REVDAT 3 29-JUL-20 2ZQO 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE
REVDAT 2 10-FEB-09 2ZQO 1 JRNL VERSN
REVDAT 1 02-SEP-08 2ZQO 0
SPRSDE 02-SEP-08 2ZQO 2AO3
JRNL AUTH R.SUZUKI,A.KUNO,T.HASEGAWA,J.HIRABAYASHI,K.KASAI,M.MOMMA,
JRNL AUTH 2 Z.FUJIMOTO
JRNL TITL SUGAR-COMPLEX STRUCTURES OF THE C-HALF DOMAIN OF THE
JRNL TITL 2 GALACTOSE-BINDING LECTIN EW29 FROM THE EARTHWORM LUMBRICUS
JRNL TITL 3 TERRESTRIS
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 49 2009
JRNL REFN ISSN 0907-4449
JRNL PMID 19153466
JRNL DOI 10.1107/S0907444908037451
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH R.SUZUKI,Z.FUJIMOTO,A.KUNO,J.HIRABAYASHI,K.KASAI,T.HASEGAWA
REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC
REMARK 1 TITL 2 STUDIES OF THE C-TERMINAL DOMAIN OF GALACTOSE-BINDING LECTIN
REMARK 1 TITL 3 EW29 FROM THE EARTHWORM LUMBRICUS TERRESTRIS
REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 1895 2004
REMARK 1 REFN ISSN 0907-4449
REMARK 1 PMID 15388944
REMARK 1 DOI 10.1107/S0907444904018979
REMARK 1 REFERENCE 2
REMARK 1 AUTH R.YABE,R.SUZUKI,A.KUNO,Z.FUJIMOTO,Y.JIGAMI,J.HIRABAYASHI
REMARK 1 TITL TAILORING A NOVEL SIALIC ACID-BINDING LECTIN FROM A RICIN-B
REMARK 1 TITL 2 CHAIN-LIKE GALACTOSE-BINDING PROTEIN BY NATURAL
REMARK 1 TITL 3 EVOLUTION-MIMICRY
REMARK 1 REF J.BIOCHEM. V. 141 389 2007
REMARK 1 REFN ISSN 0021-924X
REMARK 1 PMID 17234683
REMARK 1 DOI 10.1093/JB/MVM043
REMARK 1 REFERENCE 3
REMARK 1 AUTH J.HIRABAYASHI,S.K.DUTTA,K.KASAI
REMARK 1 TITL NOVEL GALACTOSE-BINDING PROTEINS IN ANNELIDA.
REMARK 1 TITL 2 CHARACTERIZATION OF 29-KDA TANDEM REPEAT-TYPE LECTINS FROM
REMARK 1 TITL 3 THE EARTHWORM LUMBRICUS TERRESTRIS
REMARK 1 REF J.BIOL.CHEM. V. 273 14450 1998
REMARK 1 REFN ISSN 0021-9258
REMARK 1 PMID 9603958
REMARK 1 DOI 10.1074/JBC.273.23.14450
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 48.62
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1
REMARK 3 NUMBER OF REFLECTIONS : 21951
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) : 0.195
REMARK 3 R VALUE (WORKING SET) : 0.192
REMARK 3 FREE R VALUE : 0.260
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1190
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) : 1495
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.81
REMARK 3 BIN R VALUE (WORKING SET) : 0.1920
REMARK 3 BIN FREE R VALUE SET COUNT : 85
REMARK 3 BIN FREE R VALUE : 0.2490
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2066
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 81
REMARK 3 SOLVENT ATOMS : 315
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.13
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
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): 0.161
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.766
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2204 ; 0.014 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2990 ; 1.423 ; 1.971
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 6.326 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;36.132 ;26.000
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 373 ;14.569 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.329 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 327 ; 0.095 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1650 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 999 ; 0.193 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1496 ; 0.306 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.151 ; 0.200
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): 66 ; 0.223 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.252 ; 0.200
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): 1339 ; 0.882 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2109 ; 1.437 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 988 ; 2.199 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 881 ; 3.306 ; 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 : 1.20
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
REMARK 4
REMARK 4 2ZQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-08.
REMARK 100 THE DEPOSITION ID IS D_1000028304.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-NOV-04
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-6A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23141
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 200 DATA REDUNDANCY : 7.200
REMARK 200 R MERGE (I) : 0.09800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.1000
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) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.00
REMARK 200 R MERGE FOR SHELL (I) : 0.30800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1XYF
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.73
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, DIPOTASSIUM HYDROGEN
REMARK 280 PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, IMIDAZOLE, CADMIUM
REMARK 280 CHLORIDE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -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 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.60500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.37350
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.60500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.37350
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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 B 515 LIES ON A SPECIAL POSITION.
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NZ LYS A 246 O HOH A 556 4556 2.12
REMARK 500 O HOH B 481 O HOH B 531 1545 2.15
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 ASP A 177 -167.47 -76.56
REMARK 500 ASN A 187 11.58 -143.12
REMARK 500 ASN A 217 31.61 -98.18
REMARK 500 ASN B 217 32.16 -97.73
REMARK 500
REMARK 500 REMARK: NULL
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 CD A 401 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 241 NE2
REMARK 620 2 IMD A 451 N1 93.0
REMARK 620 3 HOH A 555 O 86.7 179.4
REMARK 620 4 HOH A 557 O 85.4 90.3 90.3
REMARK 620 5 HIS B 241 NE2 175.1 91.8 88.4 95.2
REMARK 620 6 HOH B 516 O 95.0 90.1 89.4 179.5 84.4
REMARK 620 N 1 2 3 4 5
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2DRY RELATED DB: PDB
REMARK 900 LIGAND FREE FORM OF THE MUTANT LECTIN.
REMARK 900 RELATED ID: 2DRZ RELATED DB: PDB
REMARK 900 THE MUTANT LECTIN IN COMPLEX WITH LACTOSE.
REMARK 900 RELATED ID: 2DS0 RELATED DB: PDB
REMARK 900 THE MUTANT LECTIN IN COMPLEX WITH 6'-SIALYLLACTOSE.
REMARK 900 RELATED ID: 2ZQN RELATED DB: PDB
DBREF 2ZQO A 131 260 UNP O96048 O96048_LUMTE 131 260
DBREF 2ZQO B 131 260 UNP O96048 O96048_LUMTE 131 260
SEQRES 1 A 130 PRO LYS PHE PHE TYR ILE LYS SER GLU LEU ASN GLY LYS
SEQRES 2 A 130 VAL LEU ASP ILE GLU GLY GLN ASN PRO ALA PRO GLY SER
SEQRES 3 A 130 LYS ILE ILE THR TRP ASP GLN LYS LYS GLY PRO THR ALA
SEQRES 4 A 130 VAL ASN GLN LEU TRP TYR THR ASP GLN GLN GLY VAL ILE
SEQRES 5 A 130 ARG SER LYS LEU ASN ASP PHE ALA ILE ASP ALA SER HIS
SEQRES 6 A 130 GLU GLN ILE GLU THR GLN PRO PHE ASP PRO ASN ASN PRO
SEQRES 7 A 130 LYS ARG ALA TRP ILE VAL SER GLY ASN THR ILE ALA GLN
SEQRES 8 A 130 LEU SER ASP ARG ASP ILE VAL LEU ASP ILE ILE LYS SER
SEQRES 9 A 130 ASP LYS GLU ALA GLY ALA HIS ILE CYS ALA TRP LYS GLN
SEQRES 10 A 130 HIS GLY GLY PRO ASN GLN LYS PHE ILE ILE GLU SER GLU
SEQRES 1 B 130 PRO LYS PHE PHE TYR ILE LYS SER GLU LEU ASN GLY LYS
SEQRES 2 B 130 VAL LEU ASP ILE GLU GLY GLN ASN PRO ALA PRO GLY SER
SEQRES 3 B 130 LYS ILE ILE THR TRP ASP GLN LYS LYS GLY PRO THR ALA
SEQRES 4 B 130 VAL ASN GLN LEU TRP TYR THR ASP GLN GLN GLY VAL ILE
SEQRES 5 B 130 ARG SER LYS LEU ASN ASP PHE ALA ILE ASP ALA SER HIS
SEQRES 6 B 130 GLU GLN ILE GLU THR GLN PRO PHE ASP PRO ASN ASN PRO
SEQRES 7 B 130 LYS ARG ALA TRP ILE VAL SER GLY ASN THR ILE ALA GLN
SEQRES 8 B 130 LEU SER ASP ARG ASP ILE VAL LEU ASP ILE ILE LYS SER
SEQRES 9 B 130 ASP LYS GLU ALA GLY ALA HIS ILE CYS ALA TRP LYS GLN
SEQRES 10 B 130 HIS GLY GLY PRO ASN GLN LYS PHE ILE ILE GLU SER GLU
HET NGA A 270 15
HET NGA A 271 15
HET CD A 401 1
HET PO4 A 421 5
HET IMD A 451 5
HET NGA B 301 15
HET NGA B 302 15
HET PO4 B 422 5
HET PO4 B 423 5
HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE
HETNAM CD CADMIUM ION
HETNAM PO4 PHOSPHATE ION
HETNAM IMD IMIDAZOLE
HETSYN NGA N-ACETYL-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY-
HETSYN 2 NGA BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2-
HETSYN 3 NGA ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-D-GALACTOSAMINE
FORMUL 3 NGA 4(C8 H15 N O6)
FORMUL 5 CD CD 2+
FORMUL 6 PO4 3(O4 P 3-)
FORMUL 7 IMD C3 H5 N2 1+
FORMUL 12 HOH *315(H2 O)
HELIX 1 1 GLY A 149 ASN A 151 5 3
HELIX 2 2 GLY A 166 GLN A 172 5 7
HELIX 3 3 ASN A 207 ARG A 210 5 4
HELIX 4 4 LYS A 233 ASP A 235 5 3
HELIX 5 5 GLY A 250 GLN A 253 5 4
HELIX 6 6 GLY B 149 ASN B 151 5 3
HELIX 7 7 GLY B 166 GLN B 172 5 7
HELIX 8 8 ASN B 207 ARG B 210 5 4
HELIX 9 9 LYS B 233 ASP B 235 5 3
HELIX 10 10 GLY B 250 GLN B 253 5 4
SHEET 1 A 2 PHE A 134 SER A 138 0
SHEET 2 A 2 PHE A 255 SER A 259 -1 O GLU A 258 N TYR A 135
SHEET 1 B 2 VAL A 144 ILE A 147 0
SHEET 2 B 2 ILE A 158 TRP A 161 -1 O TRP A 161 N VAL A 144
SHEET 1 C 2 TRP A 174 THR A 176 0
SHEET 2 C 2 ILE A 182 SER A 184 -1 O ARG A 183 N TYR A 175
SHEET 1 D 2 ALA A 190 ASP A 192 0
SHEET 2 D 2 GLU A 199 GLN A 201 -1 O GLN A 201 N ALA A 190
SHEET 1 E 4 TRP A 212 SER A 215 0
SHEET 2 E 4 THR A 218 GLN A 221 -1 O THR A 218 N SER A 215
SHEET 3 E 4 ASP A 224 ILE A 231 -1 O LEU A 229 N ILE A 219
SHEET 4 E 4 ILE A 242 LYS A 246 -1 O CYS A 243 N ASP A 230
SHEET 1 F 2 PHE B 134 SER B 138 0
SHEET 2 F 2 PHE B 255 SER B 259 -1 O ILE B 256 N LYS B 137
SHEET 1 G 2 VAL B 144 ILE B 147 0
SHEET 2 G 2 ILE B 158 TRP B 161 -1 O TRP B 161 N VAL B 144
SHEET 1 H 2 TRP B 174 THR B 176 0
SHEET 2 H 2 ILE B 182 SER B 184 -1 O ARG B 183 N TYR B 175
SHEET 1 I 2 ALA B 190 ASP B 192 0
SHEET 2 I 2 GLU B 199 GLN B 201 -1 O GLN B 201 N ALA B 190
SHEET 1 J 4 TRP B 212 SER B 215 0
SHEET 2 J 4 THR B 218 GLN B 221 -1 O THR B 218 N SER B 215
SHEET 3 J 4 ASP B 224 ILE B 231 -1 O LEU B 229 N ILE B 219
SHEET 4 J 4 ILE B 242 LYS B 246 -1 O CYS B 243 N ASP B 230
LINK NE2 HIS A 241 CD CD A 401 1555 1555 2.28
LINK CD CD A 401 N1 IMD A 451 1555 1555 2.31
LINK CD CD A 401 O HOH A 555 1555 1555 2.30
LINK CD CD A 401 O HOH A 557 1555 1555 2.53
LINK CD CD A 401 NE2 HIS B 241 1555 1555 2.31
LINK CD CD A 401 O HOH B 516 1555 1555 2.54
CRYST1 123.210 34.747 61.586 90.00 104.20 90.00 C 1 2 1 8
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 0.008116 0.000000 0.002053 0.00000
SCALE2 0.000000 0.028779 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016749 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
