HEADER PROTEIN BINDING 13-JAN-14 4OEE TITLE CRYSTAL STRUCTURE ANALYSIS OF FGF2-DISACCHARIDE (S3I2) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 134-288; COMPND 5 SYNONYM: FGF-2, BASIC FIBROBLAST GROWTH FACTOR, BFGF, HEPARIN-BINDING COMPND 6 GROWTH FACTOR 2, HBGF-2; 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 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 5 20-SEP-23 4OEE 1 HETSYN REVDAT 4 29-JUL-20 4OEE 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 04-APR-18 4OEE 1 REMARK REVDAT 2 10-SEP-14 4OEE 1 JRNL REVDAT 1 09-JUL-14 4OEE 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 23557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.530 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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 21.1725 - 3.6086 1.00 1592 146 0.1523 0.1605 REMARK 3 2 3.6086 - 2.8665 1.00 1576 145 0.1669 0.1884 REMARK 3 3 2.8665 - 2.5048 1.00 1545 149 0.1755 0.2146 REMARK 3 4 2.5048 - 2.2761 1.00 1571 148 0.1739 0.1843 REMARK 3 5 2.2761 - 2.1131 1.00 1540 144 0.1691 0.1808 REMARK 3 6 2.1131 - 1.9886 1.00 1567 143 0.1609 0.1920 REMARK 3 7 1.9886 - 1.8891 1.00 1536 139 0.1591 0.1794 REMARK 3 8 1.8891 - 1.8069 1.00 1562 139 0.1582 0.2040 REMARK 3 9 1.8069 - 1.7374 1.00 1554 147 0.1550 0.1883 REMARK 3 10 1.7374 - 1.6775 1.00 1547 150 0.1601 0.1976 REMARK 3 11 1.6775 - 1.6250 1.00 1515 135 0.1627 0.1771 REMARK 3 12 1.6250 - 1.5786 1.00 1548 150 0.1550 0.1863 REMARK 3 13 1.5786 - 1.5371 0.99 1523 152 0.1717 0.1831 REMARK 3 14 1.5371 - 1.4996 0.89 1371 123 0.1724 0.1872 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.810 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 : 0.005 1132 REMARK 3 ANGLE : 1.104 1523 REMARK 3 CHIRALITY : 0.074 160 REMARK 3 PLANARITY : 0.005 191 REMARK 3 DIHEDRAL : 13.356 442 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 4OEE 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_1000084387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 45.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 REMARK 200 R SYM FOR SHELL (I) : 0.29300 REMARK 200 FOR SHELL : 9.800 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 (%): 43.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 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: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.22050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.06800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.22050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.06800 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 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 ALA A 144 REMARK 465 LYS A 145 REMARK 465 SER A 146 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 41 -157.51 -153.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OEF RELATED DB: PDB REMARK 900 RELATED ID: 4OEG RELATED DB: PDB DBREF 4OEE A -8 146 UNP P09038 FGF2_HUMAN 134 288 SEQADV 4OEE SER A 69 UNP P09038 CYS 211 ENGINEERED MUTATION SEQADV 4OEE 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 GNX B 2 19 HETNAM IDY 1-O-METHYL-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM GNX 2-DEOXY-3-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 GNX 2-DEOXY-3-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOSE; 2- HETSYN 2 GNX DEOXY-3-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; 2-DEOXY-3-O- HETSYN 3 GNX SULFO-2-(SULFOAMINO)-GLUCOSE FORMUL 2 IDY C7 H12 O10 S FORMUL 2 GNX C6 H13 N O11 S2 FORMUL 3 HOH *107(H2 O) HELIX 1 1 PRO A 13 ASP A 19 1 7 HELIX 2 2 THR A 89 CYS A 92 5 4 HELIX 3 3 LEU A 126 THR A 130 5 5 HELIX 4 4 GLN A 134 ILE A 137 5 4 SHEET 1 A 2 ARG A 22 CYS A 25 0 SHEET 2 A 2 PHE A 139 MET A 142 -1 O MET A 142 N ARG A 22 SHEET 1 B 2 PHE A 31 ILE A 34 0 SHEET 2 B 2 VAL A 40 VAL A 43 -1 O VAL A 43 N PHE A 31 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 ARG A 72 MET A 76 -1 O LEU A 74 N ILE A 65 SHEET 4 C 4 LEU A 82 SER A 85 -1 O SER A 85 N TYR A 73 SHEET 1 D 4 LEU A 53 GLU A 59 0 SHEET 2 D 4 VAL A 62 GLY A 67 -1 O LYS A 66 N GLN A 54 SHEET 3 D 4 PHE A 94 LEU A 98 -1 O PHE A 94 N VAL A 63 SHEET 4 D 4 ASN A 104 SER A 108 -1 O ARG A 107 N PHE A 95 LINK O4 IDY B 1 C1 GNX B 2 1555 1555 1.43 CRYST1 84.441 58.136 32.395 90.00 109.10 90.00 C 1 2 1 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 0.011843 0.000000 0.004101 0.00000 SCALE2 0.000000 0.017201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032667 0.00000