PDB Short entry for 1Q1U HEADER HORMONE/GROWTH FACTOR 22-JUL-03 1Q1U TITLE CRYSTAL STRUCTURE OF HUMAN FHF1B (FGF12B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR HOMOLOGOUS FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-144; COMPND 5 SYNONYM: FGF-12; FGF12B; FIBROBLAST GROWTH FACTOR 12 ISOFORM 2; COMPND 6 MYOCYTE-ACTIVATING FACTOR; FGF12 PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 10 OTHER_DETAILS: T7 PROMOTER DRIVEN EXPRESSION KEYWDS FGF-12; HUMAN; CRYSTAL STRUCTURE, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.K.OLSEN,M.GARBI,N.ZAMPIERI,A.V.ELISEENKOVA,D.M.ORNITZ,M.GOLDFARB, AUTHOR 2 M.MOHAMMADI REVDAT 5 16-AUG-23 1Q1U 1 REMARK REVDAT 4 27-OCT-21 1Q1U 1 REMARK SEQADV REVDAT 3 24-FEB-09 1Q1U 1 VERSN REVDAT 2 18-JAN-05 1Q1U 1 JRNL REMARK REVDAT 1 05-AUG-03 1Q1U 0 JRNL AUTH S.K.OLSEN,M.GARBI,N.ZAMPIERI,A.V.ELISEENKOVA,D.M.ORNITZ, JRNL AUTH 2 M.GOLDFARB,M.MOHAMMADI JRNL TITL FIBROBLAST GROWTH FACTOR (FGF) HOMOLOGOUS FACTORS SHARE JRNL TITL 2 STRUCTURAL BUT NOT FUNCTIONAL HOMOLOGY WITH FGFS JRNL REF J.BIOL.CHEM. V. 278 34226 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12815063 JRNL DOI 10.1074/JBC.M303183200 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12734 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 SET) : 0.223 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1307 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 : 1086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 36 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 1.310 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1Q1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 90 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) : 0.920218 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR 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 : 13171 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 ID 1IHK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 400, 200MM AMMONIUM SULFATE, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 15.31200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.70750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.42650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.70750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.31200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.42650 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 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 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 144 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 GLN A 7 CG CD OE1 NE2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 GLU A 118 CG CD OE1 OE2 REMARK 470 GLU A 142 CG CD OE1 OE2 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 LEU A 8 138.22 -28.04 REMARK 500 ASN A 92 28.16 49.82 REMARK 500 TYR A 93 -51.26 -138.66 REMARK 500 GLU A 106 -50.91 73.60 REMARK 500 GLU A 142 114.99 90.38 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 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 440 DBREF 1Q1U A 5 144 UNP P61328 FGF12_HUMAN 67 206 SEQADV 1Q1U ALA A 144 UNP P61328 CYS 206 ENGINEERED MUTATION SEQRES 1 A 144 MET GLU SER LYS GLU PRO GLN LEU LYS GLY ILE VAL THR SEQRES 2 A 144 ARG LEU PHE SER GLN GLN GLY TYR PHE LEU GLN MET HIS SEQRES 3 A 144 PRO ASP GLY THR ILE ASP GLY THR LYS ASP GLU ASN SER SEQRES 4 A 144 ASP TYR THR LEU PHE ASN LEU ILE PRO VAL GLY LEU ARG SEQRES 5 A 144 VAL VAL ALA ILE GLN GLY VAL LYS ALA SER LEU TYR VAL SEQRES 6 A 144 ALA MET ASN GLY GLU GLY TYR LEU TYR SER SER ASP VAL SEQRES 7 A 144 PHE THR PRO GLU CYS LYS PHE LYS GLU SER VAL PHE GLU SEQRES 8 A 144 ASN TYR TYR VAL ILE TYR SER SER THR LEU TYR ARG GLN SEQRES 9 A 144 GLN GLU SER GLY ARG ALA TRP PHE LEU GLY LEU ASN LYS SEQRES 10 A 144 GLU GLY GLN ILE MET LYS GLY ASN ARG VAL LYS LYS THR SEQRES 11 A 144 LYS PRO SER SER HIS PHE VAL PRO LYS PRO ILE GLU VAL SEQRES 12 A 144 ALA HET SO4 A 437 5 HET SO4 A 438 5 HET SO4 A 439 5 HET SO4 A 440 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *36(H2 O) HELIX 1 1 SER A 39 THR A 42 5 4 HELIX 2 2 THR A 80 CYS A 83 5 4 HELIX 3 3 LYS A 123 VAL A 127 5 5 HELIX 4 4 LYS A 131 SER A 134 5 4 SHEET 1 A 8 ILE A 31 THR A 34 0 SHEET 2 A 8 TYR A 21 MET A 25 -1 N PHE A 22 O THR A 34 SHEET 3 A 8 ILE A 11 SER A 17 -1 N SER A 17 O TYR A 21 SHEET 4 A 8 PHE A 44 GLY A 50 -1 O PHE A 44 N THR A 13 SHEET 5 A 8 VAL A 53 GLY A 58 -1 O GLN A 57 N ASN A 45 SHEET 6 A 8 PHE A 85 PHE A 90 -1 O PHE A 85 N VAL A 54 SHEET 7 A 8 TYR A 94 ARG A 103 -1 O TYR A 94 N PHE A 90 SHEET 8 A 8 ALA A 110 PHE A 112 -1 N TRP A 111 O SER A 99 SHEET 1 B 6 ILE A 31 THR A 34 0 SHEET 2 B 6 TYR A 21 MET A 25 -1 N PHE A 22 O THR A 34 SHEET 3 B 6 ILE A 11 SER A 17 -1 N SER A 17 O TYR A 21 SHEET 4 B 6 PHE A 136 PRO A 140 -1 O LYS A 139 N ARG A 14 SHEET 5 B 6 TYR A 94 ARG A 103 -1 N VAL A 95 O PHE A 136 SHEET 6 B 6 ALA A 110 PHE A 112 -1 N TRP A 111 O SER A 99 SHEET 1 C 2 TYR A 64 MET A 67 0 SHEET 2 C 2 LEU A 73 SER A 76 -1 O SER A 76 N TYR A 64 SITE 1 AC1 7 ARG A 52 LYS A 86 GLU A 87 SER A 88 SITE 2 AC1 7 GLN A 104 SER A 107 ARG A 109 SITE 1 AC2 7 ARG A 109 ALA A 110 PHE A 112 ASN A 125 SITE 2 AC2 7 ARG A 126 LYS A 129 HOH A 417 SITE 1 AC3 6 GLN A 19 SER A 62 LYS A 131 PRO A 132 SITE 2 AC3 6 SER A 133 HOH A 409 SITE 1 AC4 5 LEU A 51 ARG A 52 TYR A 72 LYS A 123 SITE 2 AC4 5 ARG A 126 CRYST1 30.624 58.853 65.415 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 0.032654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015287 0.00000