HEADER HORMONE/GROWTH FACTOR 29-APR-01 1IJT TITLE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 4 (FGF4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: B-TREFOIL DOMAIN; COMPND 5 SYNONYM: FGF4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS B-TREFOIL FOLD, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.BELLOSTA,A.N.PLOTNIKOV,A.V.ELISEENKOVA,C.BASILICO,M.MOHAMMADI REVDAT 4 16-AUG-23 1IJT 1 REMARK REVDAT 3 27-OCT-21 1IJT 1 REMARK SEQADV REVDAT 2 24-FEB-09 1IJT 1 VERSN REVDAT 1 15-AUG-01 1IJT 0 JRNL AUTH P.BELLOSTA,A.IWAHORI,A.N.PLOTNIKOV,A.V.ELISEENKOVA, JRNL AUTH 2 C.BASILICO,M.MOHAMMADI JRNL TITL IDENTIFICATION OF RECEPTOR AND HEPARIN BINDING SITES IN JRNL TITL 2 FIBROBLAST GROWTH FACTOR 4 BY STRUCTURE-BASED MUTAGENESIS. JRNL REF MOL.CELL.BIOL. V. 21 5946 2001 JRNL REFN ISSN 0270-7306 JRNL PMID 11486033 JRNL DOI 10.1128/MCB.21.17.5946-5957.2001 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 11488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 594 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.65000 REMARK 3 B22 (A**2) : 0.68300 REMARK 3 B33 (A**2) : 2.96700 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 0.721 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.695 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.094 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.228 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.939 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS REMARK 3 KSOL : 0.57 REMARK 3 BSOL : 74.85 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013344. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2FGF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.18350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.11550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.64750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.11550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.18350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.64750 REMARK 290 SMTRY3 4 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: MONOMERIC 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 LYS A 198 CG CD CE NZ REMARK 470 LEU A 206 CG CD1 CD2 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 ARG A 134 30.63 72.34 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 SO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IHK RELATED DB: PDB REMARK 900 1IHK IS THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 9 (FGF9) DBREF 1IJT A 79 206 UNP P08620 FGF4_HUMAN 79 206 SEQADV 1IJT GLY A 182 UNP P08620 SER 182 ENGINEERED MUTATION SEQRES 1 A 128 GLY ILE LYS ARG LEU ARG ARG LEU TYR CYS ASN VAL GLY SEQRES 2 A 128 ILE GLY PHE HIS LEU GLN ALA LEU PRO ASP GLY ARG ILE SEQRES 3 A 128 GLY GLY ALA HIS ALA ASP THR ARG ASP SER LEU LEU GLU SEQRES 4 A 128 LEU SER PRO VAL GLU ARG GLY VAL VAL SER ILE PHE GLY SEQRES 5 A 128 VAL ALA SER ARG PHE PHE VAL ALA MET SER SER LYS GLY SEQRES 6 A 128 LYS LEU TYR GLY SER PRO PHE PHE THR ASP GLU CYS THR SEQRES 7 A 128 PHE LYS GLU ILE LEU LEU PRO ASN ASN TYR ASN ALA TYR SEQRES 8 A 128 GLU SER TYR LYS TYR PRO GLY MET PHE ILE ALA LEU GLY SEQRES 9 A 128 LYS ASN GLY LYS THR LYS LYS GLY ASN ARG VAL SER PRO SEQRES 10 A 128 THR MET LYS VAL THR HIS PHE LEU PRO ARG LEU HET SO4 A 300 5 HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *96(H2 O) HELIX 1 1 THR A 111 SER A 114 5 4 HELIX 2 2 PRO A 163 ASN A 165 5 3 HELIX 3 3 LYS A 189 VAL A 193 5 5 HELIX 4 4 MET A 197 THR A 200 5 4 SHEET 1 A13 LEU A 145 SER A 148 0 SHEET 2 A13 PHE A 135 MET A 139 -1 N PHE A 136 O SER A 148 SHEET 3 A13 VAL A 125 GLY A 130 -1 O ILE A 128 N VAL A 137 SHEET 4 A13 THR A 156 LEU A 161 -1 O PHE A 157 N VAL A 126 SHEET 5 A13 ASN A 167 SER A 171 -1 O ALA A 168 N ILE A 160 SHEET 6 A13 PHE A 202 ARG A 205 -1 N PHE A 202 O ASN A 167 SHEET 7 A13 ARG A 82 CYS A 88 -1 O ARG A 85 N ARG A 205 SHEET 8 A13 PHE A 94 ALA A 98 -1 O PHE A 94 N CYS A 88 SHEET 9 A13 ILE A 104 ALA A 107 -1 O GLY A 105 N GLN A 97 SHEET 10 A13 PHE A 94 ALA A 98 -1 N HIS A 95 O ALA A 107 SHEET 11 A13 ARG A 82 CYS A 88 -1 O LEU A 86 N LEU A 96 SHEET 12 A13 LEU A 116 GLU A 122 -1 N LEU A 116 O ARG A 84 SHEET 13 A13 VAL A 125 GLY A 130 -1 O VAL A 125 N VAL A 121 SITE 1 AC1 6 GLY A 182 LYS A 183 LYS A 188 HOH A1029 SITE 2 AC1 6 HOH A1065 HOH A1066 SITE 1 AC2 9 ARG A 103 ARG A 123 GLY A 124 LYS A 144 SITE 2 AC2 9 THR A 187 HOH A1000 HOH A1033 HOH A1035 SITE 3 AC2 9 HOH A1049 SITE 1 AC3 4 GLY A 79 LYS A 81 ASP A 110 LYS A 173 CRYST1 40.367 53.295 56.231 90.00 90.00 90.00 P 21 21 21 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 0.024773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017784 0.00000