HEADER CYTOKINE 08-SEP-14 4R9W TITLE CRYSTAL STRUCTURE OF PLATELET FACTOR 4 COMPLEXED WITH FONDAPARINUX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET FACTOR 4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PF-4, C-X-C MOTIF CHEMOKINE 4, IROPLACT, ONCOSTATIN-A, COMPND 5 PLATELET FACTOR 4, SHORT FORM; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PF4, CXCL4, SCYB4; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: S2 CELLS KEYWDS PF4, FONDAPARINUX, CXC CHEMOKINE, PLATELET FACTOR, GLYCOSAMINOGLYCAN, KEYWDS 2 PLATELET, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CAI,Z.ZHU,Q.LIU,M.I.GREENE REVDAT 5 29-JUL-20 4R9W 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 HETSYN FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 22-NOV-17 4R9W 1 REMARK REVDAT 3 12-JUL-17 4R9W 1 HETSYN REVDAT 2 27-JAN-16 4R9W 1 JRNL REVDAT 1 16-DEC-15 4R9W 0 JRNL AUTH Z.CAI,S.V.YAROVOI,Z.ZHU,L.RAUOVA,V.HAYES,T.LEBEDEVA,Q.LIU, JRNL AUTH 2 M.PONCZ,G.AREPALLY,D.B.CINES,M.I.GREENE JRNL TITL ATOMIC DESCRIPTION OF THE IMMUNE COMPLEX INVOLVED IN JRNL TITL 2 HEPARIN-INDUCED THROMBOCYTOPENIA. JRNL REF NAT COMMUN V. 6 8277 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26391892 JRNL DOI 10.1038/NCOMMS9277 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 5742 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.460 REMARK 3 FREE R VALUE TEST SET COUNT : 256 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 22.7570 - 3.1489 0.98 2771 131 0.2025 0.2261 REMARK 3 2 3.1489 - 2.5000 0.99 2715 125 0.3409 0.3331 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.600 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 1083 REMARK 3 ANGLE : 0.928 1478 REMARK 3 CHIRALITY : 0.532 202 REMARK 3 PLANARITY : 0.004 163 REMARK 3 DIHEDRAL : 25.540 452 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 17.4423 20.9149 8.2694 REMARK 3 T TENSOR REMARK 3 T11: 0.3722 T22: 0.6502 REMARK 3 T33: 0.4423 T12: -0.0072 REMARK 3 T13: -0.0627 T23: 0.0908 REMARK 3 L TENSOR REMARK 3 L11: 4.9819 L22: 5.9353 REMARK 3 L33: 3.7957 L12: -0.4018 REMARK 3 L13: 1.1796 L23: 0.2278 REMARK 3 S TENSOR REMARK 3 S11: 0.2163 S12: -1.0576 S13: -0.4224 REMARK 3 S21: 0.4320 S22: 0.1495 S23: -0.2469 REMARK 3 S31: 0.2740 S32: 0.1713 S33: 0.0657 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 4R9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL BENDER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5900 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.68900 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG4000, 17% MPD, 0.1 M SODIUM REMARK 280 ACETATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.17067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.58533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.58533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.17067 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLU A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 ASP A 5 REMARK 465 GLY A 6 REMARK 465 ASP A 7 REMARK 465 SER A 70 REMARK 465 GLU B 101 REMARK 465 ALA B 102 REMARK 465 GLU B 103 REMARK 465 GLU B 104 REMARK 465 ASP B 105 REMARK 465 GLY B 106 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 LEU A 8 CG CD1 CD2 REMARK 470 HIS B 135 CG ND1 CD2 CE1 NE2 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 CYS A 12 77.39 -104.74 REMARK 500 VAL A 13 -82.67 -65.86 REMARK 500 CYS B 136 115.53 -166.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R97 RELATED DB: PDB REMARK 900 KKOFAB ONLY REMARK 900 RELATED ID: 4R9Y RELATED DB: PDB REMARK 900 KKOFAB IN COMPLEX WITH PLATELET FACTOR 4 DBREF 4R9W A 1 70 UNP P02776 PLF4_HUMAN 32 101 DBREF 4R9W B 101 170 UNP P02776 PLF4_HUMAN 32 101 SEQRES 1 A 70 GLU ALA GLU GLU ASP GLY ASP LEU GLN CYS LEU CYS VAL SEQRES 2 A 70 LYS THR THR SER GLN VAL ARG PRO ARG HIS ILE THR SER SEQRES 3 A 70 LEU GLU VAL ILE LYS ALA GLY PRO HIS CYS PRO THR ALA SEQRES 4 A 70 GLN LEU ILE ALA THR LEU LYS ASN GLY ARG LYS ILE CYS SEQRES 5 A 70 LEU ASP LEU GLN ALA PRO LEU TYR LYS LYS ILE ILE LYS SEQRES 6 A 70 LYS LEU LEU GLU SER SEQRES 1 B 70 GLU ALA GLU GLU ASP GLY ASP LEU GLN CYS LEU CYS VAL SEQRES 2 B 70 LYS THR THR SER GLN VAL ARG PRO ARG HIS ILE THR SER SEQRES 3 B 70 LEU GLU VAL ILE LYS ALA GLY PRO HIS CYS PRO THR ALA SEQRES 4 B 70 GLN LEU ILE ALA THR LEU LYS ASN GLY ARG LYS ILE CYS SEQRES 5 B 70 LEU ASP LEU GLN ALA PRO LEU TYR LYS LYS ILE ILE LYS SEQRES 6 B 70 LYS LEU LEU GLU SER HET ZDO C 1 21 HET IDS C 2 16 HET SUS C 3 23 HET BDP C 4 12 HET SGN C 5 19 HETNAM ZDO METHYL 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETNAM 2 ZDO GLUCOPYRANOSIDE HETNAM IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM SUS 2-DEOXY-3,6-DI-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETNAM 2 SUS GLUCOPYRANOSE HETNAM BDP BETA-D-GLUCOPYRANURONIC ACID HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETSYN IDS O2-SULFO-GLUCURONIC ACID HETSYN BDP D-GLUCURONIC ACID FORMUL 3 ZDO C7 H15 N O11 S2 FORMUL 3 IDS C6 H10 O10 S FORMUL 3 SUS C6 H13 N O14 S3 FORMUL 3 BDP C6 H10 O7 FORMUL 3 SGN C6 H13 N O11 S2 FORMUL 4 HOH *17(H2 O) HELIX 1 1 ARG A 20 ARG A 22 5 3 HELIX 2 2 GLN A 56 LEU A 68 1 13 HELIX 3 3 ARG B 120 ARG B 122 5 3 HELIX 4 4 PRO B 158 SER B 170 1 13 SHEET 1 A 6 LYS A 50 CYS A 52 0 SHEET 2 A 6 GLN A 40 LEU A 45 -1 N ALA A 43 O ILE A 51 SHEET 3 A 6 ILE A 24 ILE A 30 -1 N ILE A 30 O GLN A 40 SHEET 4 A 6 ILE B 124 ILE B 130 -1 O LEU B 127 N VAL A 29 SHEET 5 A 6 GLN B 140 LEU B 145 -1 O ILE B 142 N GLU B 128 SHEET 6 A 6 LYS B 150 CYS B 152 -1 O ILE B 151 N ALA B 143 SSBOND 1 CYS A 10 CYS A 36 1555 1555 2.03 SSBOND 2 CYS A 12 CYS A 52 1555 1555 2.03 SSBOND 3 CYS B 110 CYS B 136 1555 1555 2.03 SSBOND 4 CYS B 112 CYS B 152 1555 1555 2.03 LINK O4 ZDO C 1 C1 IDS C 2 1555 1555 1.43 LINK O4 IDS C 2 C1 SUS C 3 1555 1555 1.43 LINK O4 SUS C 3 C1 BDP C 4 1555 1555 1.43 LINK O4 BDP C 4 C1 SGN C 5 1555 1555 1.43 CRYST1 67.333 67.333 61.756 90.00 90.00 120.00 P 32 2 1 12 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 0.014852 0.008575 0.000000 0.00000 SCALE2 0.000000 0.017149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016193 0.00000