HEADER BLOOD CLOTTING 11-JUL-00 1F9P TITLE CRYSTAL STRUCTURE OF CONNECTIVE TISSUE ACTIVATING PEPTIDE-III(CTAP- TITLE 2 III) COMPLEXED WITH POLYVINYLSULFONIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONNECTIVE TISSUE ACTIVATING PEPTIDE-III; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CTAP-III; COMPND 5 OTHER_DETAILS: PLATELET BASIC PROTEIN N-TERMINAL TRUNCATION PRODUCT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: PLATELETS KEYWDS CHEMOKINE-HEPARIN ANALOG COMPLEX, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR J.YANG,T.FAULK,R.ASTER,G.VISENTIN,B.EDWARDS,C.CASTOR REVDAT 3 04-OCT-17 1F9P 1 REMARK REVDAT 2 24-FEB-09 1F9P 1 VERSN REVDAT 1 26-AUG-03 1F9P 0 JRNL AUTH J.YANG,T.FAULK,R.ASTER,G.VISENTIN,B.EDWARDS,C.CASTOR JRNL TITL STRUCTURE OF THE CXC CHEMOKINE, CONNECTIVE TISSUE ACTIVATING JRNL TITL 2 PEPTIDE-III, COMPLEXED WITH THE HEPARIN ANALOGUE, JRNL TITL 3 POLYVINYLSULFONIC ACID JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 585333.240 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 6734 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) : 0.232 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 735 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 819 REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 618 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.84000 REMARK 3 B22 (A**2) : 3.84000 REMARK 3 B33 (A**2) : -7.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 15.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 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) : 1.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.020 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 93.96 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : PVSA.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : PVSA.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, SODIUM ACETATE, PH 4.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 29.14500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.35000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.71750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.35000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.57250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.71750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.57250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 29.14500 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 GLU A 87 REMARK 465 SER A 88 REMARK 465 ALA A 89 REMARK 465 ASP A 90 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 GLU A 12 -3.80 87.37 REMARK 500 SER A 14 -154.54 -109.79 REMARK 500 ASP A 16 154.71 -48.31 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 ESA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ESA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ESA A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TVX RELATED DB: PDB REMARK 900 THIS IS THE STRUCTURE FOR ASP-CTAP, WHICH IS 10 AMINO ACIDS LESS REMARK 900 THAN CTAP-III AT THE N-TERMINUS REMARK 900 RELATED ID: 1NAP RELATED DB: PDB REMARK 900 THIS IS THE STRUCTURE FOR NEUTROPHIL ACTIVATING PEPTIDE-II (NAP-2), REMARK 900 WHICH IS 15 AMINO ACIDS LESS THAN CTAP-III AT THE N-TERMINUS REMARK 900 RELATED ID: 1F9Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLATELET FACTOR 4 DBREF 1F9P A 6 90 UNP P02775 PF4L_HUMAN 44 128 SEQRES 1 A 85 ASN LEU ALA LYS GLY LYS GLU GLU SER LEU ASP SER ASP SEQRES 2 A 85 LEU TYR ALA GLU LEU ARG CYS MET CYS ILE LYS THR THR SEQRES 3 A 85 SER GLY ILE HIS PRO LYS ASN ILE GLN SER LEU GLU VAL SEQRES 4 A 85 ILE GLY LYS GLY THR HIS CYS ASN GLN VAL GLU VAL ILE SEQRES 5 A 85 ALA THR LEU LYS ASP GLY ARG LYS ILE CYS LEU ASP PRO SEQRES 6 A 85 ASP ALA PRO ARG ILE LYS LYS ILE VAL GLN LYS LYS LEU SEQRES 7 A 85 ALA GLY ASP GLU SER ALA ASP HET ESA A 101 6 HET ESA A 102 6 HET ESA A 103 6 HETNAM ESA ETHANESULFONIC ACID FORMUL 2 ESA 3(C2 H6 O3 S) FORMUL 5 HOH *133(H2 O) HELIX 1 1 LEU A 19 LEU A 23 5 5 HELIX 2 2 HIS A 35 LYS A 37 5 3 HELIX 3 3 ALA A 72 ALA A 84 1 13 SHEET 1 A 3 ILE A 39 ILE A 45 0 SHEET 2 A 3 GLU A 55 LEU A 60 -1 O GLU A 55 N ILE A 45 SHEET 3 A 3 LYS A 65 LEU A 68 -1 O ILE A 66 N ALA A 58 SSBOND 1 CYS A 25 CYS A 51 1555 1555 2.04 SSBOND 2 CYS A 27 CYS A 67 1555 1555 2.03 LINK C2 ESA A 101 C1 ESA A 102 1555 1555 1.54 LINK C2 ESA A 102 C1 ESA A 103 1555 1555 1.54 SITE 1 AC1 5 HIS A 35 PRO A 36 ARG A 74 ESA A 102 SITE 2 AC1 5 ESA A 103 SITE 1 AC2 4 HIS A 35 LYS A 37 ESA A 101 ESA A 103 SITE 1 AC3 7 HIS A 35 PRO A 36 LYS A 37 LYS A 81 SITE 2 AC3 7 ESA A 101 ESA A 102 HOH A 324 CRYST1 54.700 54.700 58.290 90.00 90.00 90.00 P 43 21 2 8 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 0.018282 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017156 0.00000