HEADER GROWTH FACTOR 27-OCT-04 1WAQ
TITLE CRYSTAL STRUCTURE OF HUMAN GROWTH AND DIFFERENTIATION FACTOR 5 (GDF-5)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GROWTH/DIFFERENTIATION FACTOR 5;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 387-501 (RESIDUES 6-120 OF MATURE GDF-5);
COMPND 5 SYNONYM: GDF-5, CARTILAGE-DERIVED MORPHOGENETIC PROTEIN 1, CDMP-1;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: DIMERIC CONNECTED THROUGH INTERMOLECULAR DISULFIDE
COMPND 8 BOND BETWEEN CYS 84
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 CELL: FIBROBLAST;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: RBSIIN25X/O
KEYWDS GROWTH FACTOR, TGF-BETA SUPERFAMILY, CYTOKINE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.D.MUELLER,J.NICKEL,W.SEBALD
REVDAT 5 13-DEC-23 1WAQ 1 REMARK
REVDAT 4 13-JUL-11 1WAQ 1 VERSN
REVDAT 3 24-FEB-09 1WAQ 1 VERSN
REVDAT 2 08-JUN-05 1WAQ 1 JRNL REMARK
REVDAT 1 19-MAY-05 1WAQ 0
JRNL AUTH J.NICKEL,A.KOTZSCH,W.SEBALD,T.D.MUELLER
JRNL TITL A SINGLE RESIDUE OF GDF-5 DEFINES BINDING SPECIFICITY TO BMP
JRNL TITL 2 RECEPTOR IB.
JRNL REF J.MOL.BIOL. V. 349 933 2005
JRNL REFN ISSN 0022-2836
JRNL PMID 15890363
JRNL DOI 10.1016/J.JMB.2005.04.015
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH S.KELLER,J.NICKEL,W.SEBALD,T.D.MUELLER
REMARK 1 TITL MOLECULAR RECOGNITION OF BMP-2 AND BMP RECEPTOR IA
REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 11 481 2004
REMARK 1 REFN ISSN 1545-9993
REMARK 1 PMID 15064755
REMARK 1 DOI 10.1038/NSMB756
REMARK 2
REMARK 2 RESOLUTION. 2.28 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.24
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) : 2.28
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 3 NUMBER OF REFLECTIONS : 10300
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) : 0.223
REMARK 3 R VALUE (WORKING SET) : 0.222
REMARK 3 FREE R VALUE : 0.237
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 546
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) : 2.28
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34
REMARK 3 REFLECTION IN BIN (WORKING SET) : 645
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2890
REMARK 3 BIN FREE R VALUE SET COUNT : 35
REMARK 3 BIN FREE R VALUE : 0.2970
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 825
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 24
REMARK 3 SOLVENT ATOMS : 23
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.71
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.09000
REMARK 3 B22 (A**2) : 0.09000
REMARK 3 B33 (A**2) : -0.14000
REMARK 3 B12 (A**2) : 0.05000
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): 0.187
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.508
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 877 ; 0.017 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1197 ; 1.412 ; 1.971
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 103 ; 6.457 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 130 ; 0.095 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 659 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 337 ; 0.212 ; 0.300
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): 52 ; 0.186 ; 0.500
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): 44 ; 0.266 ; 0.300
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.194 ; 0.500
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): 525 ; 9.014 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 858 ;11.061 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 352 ;14.125 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 339 ;17.954 ; 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 : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 17 A 120
REMARK 3 ORIGIN FOR THE GROUP (A): 96.0070 92.4030 88.6540
REMARK 3 T TENSOR
REMARK 3 T11: 0.1577 T22: 0.0609
REMARK 3 T33: 0.0145 T12: 0.0177
REMARK 3 T13: -0.0240 T23: 0.0226
REMARK 3 L TENSOR
REMARK 3 L11: 1.5191 L22: 21.7989
REMARK 3 L33: 1.1117 L12: 4.9477
REMARK 3 L13: -0.8447 L23: -2.1301
REMARK 3 S TENSOR
REMARK 3 S11: -0.1208 S12: 0.0873 S13: 0.1941
REMARK 3 S21: -1.2863 S22: 0.1412 S23: 0.7956
REMARK 3 S31: 0.0089 S32: -0.0100 S33: -0.0204
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH 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. RESIDUES 6 TO 16 OF THE MATURE PART OF GDF-5 ARE
REMARK 3 DISORDERED
REMARK 4
REMARK 4 1WAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-04.
REMARK 100 THE DEPOSITION ID IS D_1290021417.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-AUG-02
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9183
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11084
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280
REMARK 200 RESOLUTION RANGE LOW (A) : 84.520
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 200 DATA REDUNDANCY : 4.500
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : 0.19000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 1BMP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 72.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% 2-METHLY-2,4-PENTANEDIOL, 0.1M
REMARK 280 SODIUM CITRATE PH 4.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.88333
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.44167
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 14.44167
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.88333
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PQS
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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 169.34434
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 187.74167
REMARK 400
REMARK 400 COMPOUND
REMARK 400 COULD BE INVOLVED IN BONE FORMATION.
REMARK 400 HOMODIMER; DISULFIDE-LINKED (BY SIMILARITY).
REMARK 400 DEFECTS IN GDF5 ARE THE CAUSE OF CHONDRODYSPLASIA GREBE.
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 MET A 4
REMARK 465 LYS A 5
REMARK 465 ARG A 6
REMARK 465 GLN A 7
REMARK 465 GLY A 8
REMARK 465 LYS A 9
REMARK 465 ARG A 10
REMARK 465 PRO A 11
REMARK 465 SER A 12
REMARK 465 LYS A 13
REMARK 465 ASN A 14
REMARK 465 LEU A 15
REMARK 465 LYS A 16
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 ARG A 57 CZ ARG A 57 NH1 0.141
REMARK 500 TYR A 106 CZ TYR A 106 CE2 0.083
REMARK 500 TYR A 106 CE2 TYR A 106 CD2 0.165
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES
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 PHE A 46 164.00 63.02
REMARK 500 GLU A 61 60.17 29.89
REMARK 500 ASP A 76 84.98 -154.09
REMARK 500 THR A 83 -179.92 -69.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1121
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1122
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1123
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2BHK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN GROWTH AND DIFFERENTIATION FACTOR 5
REMARK 900 (GDF5)
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES 6 TO 120 OF MATURE GDF-5 WERE EXPRESSED WITH AN N-
REMARK 999 TERMINAL EXTENSION MET-LYS FROM THE EXPRESSION VECTOR
DBREF 1WAQ A 4 5 PDB 1WAQ 1WAQ 4 5
DBREF 1WAQ A 6 120 UNP P43026 GDF5_HUMAN 387 501
SEQRES 1 A 117 MET LYS ARG GLN GLY LYS ARG PRO SER LYS ASN LEU LYS
SEQRES 2 A 117 ALA ARG CYS SER ARG LYS ALA LEU HIS VAL ASN PHE LYS
SEQRES 3 A 117 ASP MET GLY TRP ASP ASP TRP ILE ILE ALA PRO LEU GLU
SEQRES 4 A 117 TYR GLU ALA PHE HIS CYS GLU GLY LEU CYS GLU PHE PRO
SEQRES 5 A 117 LEU ARG SER HIS LEU GLU PRO THR ASN HIS ALA VAL ILE
SEQRES 6 A 117 GLN THR LEU MET ASN SER MET ASP PRO GLU SER THR PRO
SEQRES 7 A 117 PRO THR CYS CYS VAL PRO THR ARG LEU SER PRO ILE SER
SEQRES 8 A 117 ILE LEU PHE ILE ASP SER ALA ASN ASN VAL VAL TYR LYS
SEQRES 9 A 117 GLN TYR GLU ASP MET VAL VAL GLU SER CYS GLY CYS ARG
HET MPD A1121 8
HET MPD A1122 8
HET MPD A1123 8
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
FORMUL 2 MPD 3(C6 H14 O2)
FORMUL 5 HOH *23(H2 O)
HELIX 1 1 ARG A 57 GLU A 61 5 5
HELIX 2 2 THR A 63 ASP A 76 1 14
SHEET 1 AA 2 SER A 20 LYS A 22 0
SHEET 2 AA 2 HIS A 47 GLU A 49 -1 O HIS A 47 N LYS A 22
SHEET 1 AB 2 HIS A 25 ASN A 27 0
SHEET 2 AB 2 GLU A 42 GLU A 44 -1 O TYR A 43 N VAL A 26
SHEET 1 AC 3 ILE A 37 ALA A 39 0
SHEET 2 AC 3 CYS A 85 ILE A 98 -1 O LEU A 96 N ILE A 38
SHEET 3 AC 3 VAL A 104 CYS A 119 -1 O VAL A 105 N PHE A 97
SSBOND 1 CYS A 19 CYS A 85 1555 1555 2.05
SSBOND 2 CYS A 48 CYS A 117 1555 1555 2.05
SSBOND 3 CYS A 52 CYS A 119 1555 1555 2.07
SSBOND 4 CYS A 84 CYS A 84 1555 5679 2.50
CISPEP 1 ALA A 39 PRO A 40 0 -6.06
CISPEP 2 PHE A 54 PRO A 55 0 0.60
SITE 1 AC1 4 TRP A 33 TRP A 36 PHE A 97 TYR A 109
SITE 1 AC2 2 ASN A 64 VAL A 67
SITE 1 AC3 4 ASP A 34 ASP A 35 ILE A 37 ILE A 98
CRYST1 97.771 97.771 43.325 90.00 90.00 120.00 P 32 2 1 6
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 0.010228 0.005905 0.000000 0.00000
SCALE2 0.000000 0.011810 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023081 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
