HEADER PROTEIN BINDING 13-JAN-14 4OEF TITLE CRYSTAL STRUCTURE ANALYSIS OF FGF2-DISACCHARIDE (S6I2) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FGF-2, BASIC FIBROBLAST GROWTH FACTOR, BFGF, HEPARIN-BINDING COMPND 5 GROWTH FACTOR 2, HBGF-2; 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: FGF2, FGFB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(RIPL); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS HEPARIN/HEPARIN SULFATE BINDING, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.LI,C.D.HSIAO REVDAT 4 20-SEP-23 4OEF 1 HETSYN REVDAT 3 29-JUL-20 4OEF 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 10-SEP-14 4OEF 1 JRNL REVDAT 1 09-JUL-14 4OEF 0 JRNL AUTH Y.C.LI,I.H.HO,C.C.KU,Y.Q.ZHONG,Y.P.HU,Z.G.CHEN,C.Y.CHEN, JRNL AUTH 2 W.C.LIN,M.M.ZULUETA,S.C.HUNG,M.G.LIN,C.C.WANG,C.D.HSIAO JRNL TITL INTERACTIONS THAT INFLUENCE THE BINDING OF SYNTHETIC HEPARAN JRNL TITL 2 SULFATE BASED DISACCHARIDES TO FIBROBLAST GROWTH FACTOR-2. JRNL REF ACS CHEM.BIOL. V. 9 1712 2014 JRNL REFN ISSN 1554-8929 JRNL PMID 24959968 JRNL DOI 10.1021/CB500298Q REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 10464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.3061 - 3.4353 0.98 1416 158 0.1492 0.1907 REMARK 3 2 3.4353 - 2.7279 0.97 1378 153 0.1787 0.2281 REMARK 3 3 2.7279 - 2.3834 0.95 1365 152 0.1903 0.2272 REMARK 3 4 2.3834 - 2.1656 0.94 1334 148 0.1708 0.2247 REMARK 3 5 2.1656 - 2.0105 0.93 1354 151 0.1617 0.2512 REMARK 3 6 2.0105 - 1.8920 0.92 1301 145 0.1797 0.2395 REMARK 3 7 1.8920 - 1.7973 0.89 1269 140 0.2006 0.2660 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.120 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1068 REMARK 3 ANGLE : 1.197 1436 REMARK 3 CHIRALITY : 0.083 152 REMARK 3 PLANARITY : 0.004 179 REMARK 3 DIHEDRAL : 15.090 418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 36.2000 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : 0.27400 REMARK 200 FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1BFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% POLYETHYLENE GLYCOL 600 AND 100 MM REMARK 280 NA2HPO4/CITRIC ACID, PH 4.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 299K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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, B 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 -8 REMARK 465 ALA A -7 REMARK 465 ALA A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 ILE A -3 REMARK 465 THR A -2 REMARK 465 THR A -1 REMARK 465 LEU A 0 REMARK 465 PRO A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 PRO A 13 REMARK 465 PRO A 14 REMARK 465 GLY A 15 REMARK 465 HIS A 16 REMARK 465 PHE A 17 REMARK 465 LYS A 18 REMARK 465 ALA A 144 REMARK 465 LYS A 145 REMARK 465 SER A 146 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OEE RELATED DB: PDB REMARK 900 RELATED ID: 4OEG RELATED DB: PDB DBREF 4OEF A -8 146 UNP P09038 FGF2_HUMAN 134 288 SEQADV 4OEF SER A 69 UNP P09038 CYS 211 ENGINEERED MUTATION SEQADV 4OEF SER A 87 UNP P09038 CYS 229 ENGINEERED MUTATION SEQRES 1 A 155 MET ALA ALA GLY SER ILE THR THR LEU PRO ALA LEU PRO SEQRES 2 A 155 GLU ASP GLY GLY SER GLY ALA PHE PRO PRO GLY HIS PHE SEQRES 3 A 155 LYS ASP PRO LYS ARG LEU TYR CYS LYS ASN GLY GLY PHE SEQRES 4 A 155 PHE LEU ARG ILE HIS PRO ASP GLY ARG VAL ASP GLY VAL SEQRES 5 A 155 ARG GLU LYS SER ASP PRO HIS ILE LYS LEU GLN LEU GLN SEQRES 6 A 155 ALA GLU GLU ARG GLY VAL VAL SER ILE LYS GLY VAL SER SEQRES 7 A 155 ALA ASN ARG TYR LEU ALA MET LYS GLU ASP GLY ARG LEU SEQRES 8 A 155 LEU ALA SER LYS SER VAL THR ASP GLU CYS PHE PHE PHE SEQRES 9 A 155 GLU ARG LEU GLU SER ASN ASN TYR ASN THR TYR ARG SER SEQRES 10 A 155 ARG LYS TYR THR SER TRP TYR VAL ALA LEU LYS ARG THR SEQRES 11 A 155 GLY GLN TYR LYS LEU GLY SER LYS THR GLY PRO GLY GLN SEQRES 12 A 155 LYS ALA ILE LEU PHE LEU PRO MET SER ALA LYS SER HET IDY B 1 18 HET SGN B 2 19 HETNAM IDY 1-O-METHYL-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETSYN IDY METHYL 2-O-SULFO-ALPHA-L-IDOPYRANOSIDURONIC ACID; 1-O- HETSYN 2 IDY METHYL-2-O-SULFO-ALPHA-L-IDURONIC ACID; 1-O-METHYL-2- HETSYN 3 IDY O-SULFO-L-IDURONIC ACID; 1-O-METHYL-2-O-SULFO-IDURONIC HETSYN 4 IDY ACID HETSYN SGN N,O6-DISULFO-GLUCOSAMINE; 6-O-SULFO-N-SULFO-ALPHA-D- HETSYN 2 SGN GLUCOSAMINE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETSYN 3 SGN GLUCOSE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; HETSYN 4 SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-GLUCOSE FORMUL 2 IDY C7 H12 O10 S FORMUL 2 SGN C6 H13 N O11 S2 FORMUL 3 HOH *95(H2 O) HELIX 1 1 THR A 89 CYS A 92 5 4 HELIX 2 2 LEU A 126 THR A 130 5 5 HELIX 3 3 GLN A 134 ILE A 137 5 4 SHEET 1 A 4 VAL A 40 VAL A 43 0 SHEET 2 A 4 PHE A 30 ILE A 34 -1 N PHE A 31 O VAL A 43 SHEET 3 A 4 ARG A 22 CYS A 25 -1 N CYS A 25 O PHE A 30 SHEET 4 A 4 PHE A 139 MET A 142 -1 O MET A 142 N ARG A 22 SHEET 1 B 4 LEU A 53 GLU A 59 0 SHEET 2 B 4 VAL A 62 GLY A 67 -1 O LYS A 66 N GLN A 54 SHEET 3 B 4 ARG A 72 MET A 76 -1 O LEU A 74 N ILE A 65 SHEET 4 B 4 LEU A 82 SER A 85 -1 O SER A 85 N TYR A 73 SHEET 1 C 4 LEU A 53 GLU A 59 0 SHEET 2 C 4 VAL A 62 GLY A 67 -1 O LYS A 66 N GLN A 54 SHEET 3 C 4 PHE A 94 LEU A 98 -1 O PHE A 94 N VAL A 63 SHEET 4 C 4 ASN A 104 SER A 108 -1 O ARG A 107 N PHE A 95 LINK O4 IDY B 1 C1 SGN B 2 1555 1555 1.44 CRYST1 30.417 33.083 35.608 65.52 72.60 77.35 P 1 1 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 0.032876 -0.007377 -0.008128 0.00000 SCALE2 0.000000 0.030979 -0.012524 0.00000 SCALE3 0.000000 0.000000 0.031744 0.00000