PDB Short entry for 3B9U HEADER HORMONE 06-NOV-07 3B9U TITLE CRYSTAL STRUCTURE OF L26N/D28N/H93G MUTANT OF HUMAN ACIDIC FIBROBLAST TITLE 2 GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPARIN-BINDING GROWTH FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HBGF-1, ACIDIC FIBROBLAST GROWTH FACTOR, AFGF, BETA- COMPND 5 ENDOTHELIAL CELL GROWTH FACTOR, ECGF-BETA; 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 GENE: FGF1, FGFA; 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: PET21A(+) KEYWDS BETA-TREFOIL, ACETYLATION, ANGIOGENESIS, DEVELOPMENTAL PROTEIN, KEYWDS 2 DIFFERENTIATION, GROWTH FACTOR, HEPARIN-BINDING, MITOGEN, KEYWDS 3 POLYMORPHISM, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR M.BLABER,J.LEE REVDAT 4 30-AUG-23 3B9U 1 REMARK REVDAT 3 20-OCT-21 3B9U 1 REMARK SEQADV REVDAT 2 24-FEB-09 3B9U 1 VERSN REVDAT 1 15-APR-08 3B9U 0 JRNL AUTH J.LEE,V.K.DUBEY,L.M.LONGO,M.BLABER JRNL TITL A LOGICAL OR REDUNDANCY WITHIN THE ASX-PRO-ASX-GLY TYPE I JRNL TITL 2 BETA-TURN MOTIF. JRNL REF J.MOL.BIOL. V. 377 1251 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18308335 JRNL DOI 10.1016/J.JMB.2008.01.055 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 161691.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 17570 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) : 0.191 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 845 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1781 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 84 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : -2.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.35000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.310 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 44.92 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3B9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 103 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 : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17570 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 32.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.020 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 1K5U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.15K 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 22.09500 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 PHE A 1 REMARK 465 ASN A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 5 REMARK 465 GLY A 6 REMARK 465 SER A 139 REMARK 465 ASP A 140 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 ASP A 32 -157.87 -153.26 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 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K5U RELATED DB: PDB REMARK 900 HUMAN ACIDIC FIBROBLAST GROWTH FACTOR. 141 AMINO ACID FORM WITH REMARK 900 AMINO TERMINAL HIS TAG WITH HIS93 REPLACED BY GLY DBREF 3B9U A 1 140 UNP P05230 FGF1_HUMAN 16 155 SEQADV 3B9U HIS A -5 UNP P05230 EXPRESSION TAG SEQADV 3B9U HIS A -4 UNP P05230 EXPRESSION TAG SEQADV 3B9U HIS A -3 UNP P05230 EXPRESSION TAG SEQADV 3B9U HIS A -2 UNP P05230 EXPRESSION TAG SEQADV 3B9U HIS A -1 UNP P05230 EXPRESSION TAG SEQADV 3B9U HIS A 0 UNP P05230 EXPRESSION TAG SEQADV 3B9U ASN A 26 UNP P05230 LEU 41 ENGINEERED MUTATION SEQADV 3B9U ASN A 28 UNP P05230 ASP 43 ENGINEERED MUTATION SEQADV 3B9U GLY A 93 UNP P05230 HIS 108 ENGINEERED MUTATION SEQRES 1 A 146 HIS HIS HIS HIS HIS HIS PHE ASN LEU PRO PRO GLY ASN SEQRES 2 A 146 TYR LYS LYS PRO LYS LEU LEU TYR CYS SER ASN GLY GLY SEQRES 3 A 146 HIS PHE LEU ARG ILE ASN PRO ASN GLY THR VAL ASP GLY SEQRES 4 A 146 THR ARG ASP ARG SER ASP GLN HIS ILE GLN LEU GLN LEU SEQRES 5 A 146 SER ALA GLU SER VAL GLY GLU VAL TYR ILE LYS SER THR SEQRES 6 A 146 GLU THR GLY GLN TYR LEU ALA MET ASP THR ASP GLY LEU SEQRES 7 A 146 LEU TYR GLY SER GLN THR PRO ASN GLU GLU CYS LEU PHE SEQRES 8 A 146 LEU GLU ARG LEU GLU GLU ASN GLY TYR ASN THR TYR ILE SEQRES 9 A 146 SER LYS LYS HIS ALA GLU LYS ASN TRP PHE VAL GLY LEU SEQRES 10 A 146 LYS LYS ASN GLY SER CYS LYS ARG GLY PRO ARG THR HIS SEQRES 11 A 146 TYR GLY GLN LYS ALA ILE LEU PHE LEU PRO LEU PRO VAL SEQRES 12 A 146 SER SER ASP HET SO4 A 141 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *100(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 HELIX 2 2 ASN A 80 CYS A 83 5 4 HELIX 3 3 HIS A 102 ASN A 106 5 5 HELIX 4 4 ARG A 119 THR A 123 5 5 HELIX 5 5 GLN A 127 ILE A 130 5 4 SHEET 1 A 4 VAL A 31 THR A 34 0 SHEET 2 A 4 HIS A 21 ILE A 25 -1 N ARG A 24 O ASP A 32 SHEET 3 A 4 LYS A 12 CYS A 16 -1 N CYS A 16 O HIS A 21 SHEET 4 A 4 PHE A 132 PRO A 136 -1 O LEU A 135 N LEU A 13 SHEET 1 B 4 LEU A 44 SER A 50 0 SHEET 2 B 4 GLU A 53 SER A 58 -1 O LYS A 57 N GLN A 45 SHEET 3 B 4 PHE A 85 LEU A 89 -1 O PHE A 85 N VAL A 54 SHEET 4 B 4 ASN A 95 SER A 99 -1 O ILE A 98 N LEU A 86 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 5 ASN A 18 LYS A 112 LYS A 113 LYS A 118 SITE 2 AC1 5 HOH A 157 CRYST1 33.389 44.190 47.957 90.00 100.45 90.00 P 1 21 1 2 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 0.029950 0.000000 0.005524 0.00000 SCALE2 0.000000 0.022630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021204 0.00000