HEADER STRUCTURAL PROTEIN 02-DEC-04 1WU9
TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE END-BINDING PROTEIN
TITLE 2 1 (EB1)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN;
COMPND 5 SYNONYM: APC-BINDING PROTEIN EB1;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: EB1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B
KEYWDS EB1-LIKE STRUCTURAL MOTIF, APC/DYNACTIN BINDING DOMAIN, COILED COIL,
KEYWDS 2 STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.HONNAPPA,C.M.JOHN,D.KOSTREWA,F.K.WINKLER,M.O.STEINMETZ
REVDAT 4 13-MAR-24 1WU9 1 SEQADV
REVDAT 3 11-OCT-17 1WU9 1 REMARK
REVDAT 2 24-FEB-09 1WU9 1 VERSN
REVDAT 1 01-FEB-05 1WU9 0
JRNL AUTH S.HONNAPPA,C.M.JOHN,D.KOSTREWA,F.K.WINKLER,M.O.STEINMETZ
JRNL TITL STRUCTURAL INSIGHTS INTO THE EB1-APC INTERACTION
JRNL REF EMBO J. V. 24 261 2005
JRNL REFN ISSN 0261-4189
JRNL PMID 15616574
JRNL DOI 10.1038/SJ.EMBOJ.7600529
REMARK 2
REMARK 2 RESOLUTION. 1.54 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.9999
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.23
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 17745
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) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.220
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 959
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) : 1.54
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1155
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2680
REMARK 3 BIN FREE R VALUE SET COUNT : 57
REMARK 3 BIN FREE R VALUE : 0.3430
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1030
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 119
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.60000
REMARK 3 B22 (A**2) : -0.24000
REMARK 3 B33 (A**2) : -1.60000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.45000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.085
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.675
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1040 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 951 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1404 ; 1.177 ; 1.978
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2221 ; 0.743 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 124 ; 4.098 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;29.553 ;26.613
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 198 ;12.891 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ; 8.410 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 161 ; 0.063 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1156 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 186 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 247 ; 0.227 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 963 ; 0.158 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 621 ; 0.084 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 57 ; 0.170 ; 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): 23 ; 0.205 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 76 ; 0.202 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.161 ; 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): 831 ; 2.625 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 258 ; 0.643 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1014 ; 2.836 ; 3.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 460 ; 5.634 ; 4.500
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 390 ; 7.641 ; 6.000
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 1WU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000024005.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-APR-04
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC MIRRORS
REMARK 200 OPTICS : OSMIC MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18705
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540
REMARK 200 RESOLUTION RANGE LOW (A) : 55.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.04000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1
REMARK 200 DATA REDUNDANCY IN SHELL : 2.40
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.18800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 30.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, PEG 3350, GAMMA
REMARK 280 -BUTYROLACTONE, PH 4.5, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 18.65000
REMARK 290 SMTRY3 2 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 300 REMARK: THE BIOLOGICAL UNIT IS THE DIMER IN THE ASYMMETRIC UNIT.
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3000 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8620 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A 189
REMARK 465 SER A 190
REMARK 465 ASP A 250
REMARK 465 GLU A 251
REMARK 465 GLY A 252
REMARK 465 PHE A 253
REMARK 465 VAL A 254
REMARK 465 ILE A 255
REMARK 465 PRO A 256
REMARK 465 ASP A 257
REMARK 465 GLU A 258
REMARK 465 GLY A 259
REMARK 465 GLY A 260
REMARK 465 PRO A 261
REMARK 465 GLN A 262
REMARK 465 GLU A 263
REMARK 465 GLU A 264
REMARK 465 GLN A 265
REMARK 465 GLU A 266
REMARK 465 GLU A 267
REMARK 465 TYR A 268
REMARK 465 GLY B 189
REMARK 465 SER B 190
REMARK 465 GLU B 258
REMARK 465 GLY B 259
REMARK 465 GLY B 260
REMARK 465 PRO B 261
REMARK 465 GLN B 262
REMARK 465 GLU B 263
REMARK 465 GLU B 264
REMARK 465 GLN B 265
REMARK 465 GLU B 266
REMARK 465 GLU B 267
REMARK 465 TYR B 268
DBREF 1WU9 A 191 268 UNP Q15691 MARE1_HUMAN 190 267
DBREF 1WU9 B 191 268 UNP Q15691 MARE1_HUMAN 190 267
SEQADV 1WU9 GLY A 189 UNP Q15691 CLONING ARTIFACT
SEQADV 1WU9 SER A 190 UNP Q15691 CLONING ARTIFACT
SEQADV 1WU9 GLY B 189 UNP Q15691 CLONING ARTIFACT
SEQADV 1WU9 SER B 190 UNP Q15691 CLONING ARTIFACT
SEQRES 1 A 80 GLY SER ASP GLU ALA ALA GLU LEU MET GLN GLN VAL ASN
SEQRES 2 A 80 VAL LEU LYS LEU THR VAL GLU ASP LEU GLU LYS GLU ARG
SEQRES 3 A 80 ASP PHE TYR PHE GLY LYS LEU ARG ASN ILE GLU LEU ILE
SEQRES 4 A 80 CYS GLN GLU ASN GLU GLY GLU ASN ASP PRO VAL LEU GLN
SEQRES 5 A 80 ARG ILE VAL ASP ILE LEU TYR ALA THR ASP GLU GLY PHE
SEQRES 6 A 80 VAL ILE PRO ASP GLU GLY GLY PRO GLN GLU GLU GLN GLU
SEQRES 7 A 80 GLU TYR
SEQRES 1 B 80 GLY SER ASP GLU ALA ALA GLU LEU MET GLN GLN VAL ASN
SEQRES 2 B 80 VAL LEU LYS LEU THR VAL GLU ASP LEU GLU LYS GLU ARG
SEQRES 3 B 80 ASP PHE TYR PHE GLY LYS LEU ARG ASN ILE GLU LEU ILE
SEQRES 4 B 80 CYS GLN GLU ASN GLU GLY GLU ASN ASP PRO VAL LEU GLN
SEQRES 5 B 80 ARG ILE VAL ASP ILE LEU TYR ALA THR ASP GLU GLY PHE
SEQRES 6 B 80 VAL ILE PRO ASP GLU GLY GLY PRO GLN GLU GLU GLN GLU
SEQRES 7 B 80 GLU TYR
FORMUL 3 HOH *119(H2 O)
HELIX 1 1 ASP A 191 ASN A 231 1 41
HELIX 2 2 ASP A 236 ALA A 248 1 13
HELIX 3 3 ASP B 191 ASN B 231 1 41
HELIX 4 4 ASP B 236 TYR B 247 1 12
HELIX 5 5 ALA B 248 VAL B 254 5 7
CRYST1 32.000 37.300 56.500 90.00 105.40 90.00 P 1 21 1 4
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 0.031292 0.000000 0.008625 0.00000
SCALE2 0.000000 0.026792 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018375 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
