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 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 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