HEADER TOXIN 04-SEP-01 1JWI TITLE CRYSTAL STRUCTURE OF BITISCETIN, A VON WILLEBAND FACTOR-DEPENDENT TITLE 2 PLATELET AGGREGATION INDUCER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BITISCETIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BITISCETIN ALPHA CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PLATELET AGGREGATION INDUCER; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: BITISCETIN BETA CHAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BITIS ARIETANS; SOURCE 3 ORGANISM_COMMON: PUFF ADDER; SOURCE 4 ORGANISM_TAXID: 8692; SOURCE 5 SECRETION: VENOM; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: BITIS ARIETANS; SOURCE 8 ORGANISM_COMMON: PUFF ADDER; SOURCE 9 ORGANISM_TAXID: 8692; SOURCE 10 SECRETION: VENOM KEYWDS DOMAIN SWAPPING, C-TYPE LECTIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR S.HIROTSU,H.MIZUNO,K.FUKUDA,M.C.QI,T.MATSUI,J.HAMAKO,T.MORITA, AUTHOR 2 K.TITANI REVDAT 4 25-OCT-23 1JWI 1 REMARK REVDAT 3 24-FEB-09 1JWI 1 VERSN REVDAT 2 18-DEC-02 1JWI 1 REMARK REVDAT 1 28-NOV-01 1JWI 0 JRNL AUTH S.HIROTSU,H.MIZUNO,K.FUKUDA,M.C.QI,T.MATSUI,J.HAMAKO, JRNL AUTH 2 T.MORITA,K.TITANI JRNL TITL CRYSTAL STRUCTURE OF BITISCETIN, A VON WILLEBRAND JRNL TITL 2 FACTOR-DEPENDENT PLATELET AGGREGATION INDUCER. JRNL REF BIOCHEMISTRY V. 40 13592 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11695907 JRNL DOI 10.1021/BI0114933 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 457829.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 18040 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) : 0.207 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1750 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2593 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 289 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : 5.63000 REMARK 3 B33 (A**2) : -5.80000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 60.85 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 2000 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 8.5 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 ULTRAX 18 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MIRRORS REMARK 200 OPTICS : CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 566351 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 65.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 30.30 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : 0.26400 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1BJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CALCIUM CHLORIDE, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.67500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.46500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.46500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.67500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.87000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 ASP A 1 REMARK 465 PRO A 2 REMARK 465 GLY A 3 REMARK 465 THR A 60 REMARK 465 LYS A 61 REMARK 465 ARG A 128 REMARK 465 LEU A 129 REMARK 465 PRO A 130 REMARK 465 HIS A 131 REMARK 465 ASP B 1 REMARK 465 GLU B 2 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 LYS A 12 52.00 37.29 REMARK 500 ASN A 35 34.11 -98.79 REMARK 500 ASN A 93 47.74 -140.84 REMARK 500 TYR B 11 118.79 -161.39 REMARK 500 ASP B 88 -78.57 -92.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JWI A 1 131 GB 2134244 JC5058 1 131 DBREF 1JWI B 1 125 GB 2134245 JC5059 1 125 SEQRES 1 A 131 ASP PRO GLY CYS LEU PRO ASP TRP SER SER TYR LYS GLY SEQRES 2 A 131 HIS CYS TYR LYS VAL PHE LYS LYS VAL GLY THR TRP GLU SEQRES 3 A 131 ASP ALA GLU LYS PHE CYS VAL GLU ASN SER GLY HIS LEU SEQRES 4 A 131 ALA SER ILE ASP SER LYS GLU GLU ALA ASP PHE VAL THR SEQRES 5 A 131 LYS LEU ALA SER GLN THR LEU THR LYS PHE VAL TYR ASP SEQRES 6 A 131 ALA TRP ILE GLY LEU ARG ASP GLU SER LYS THR GLN GLN SEQRES 7 A 131 CYS SER PRO GLN TRP THR ASP GLY SER SER VAL VAL TYR SEQRES 8 A 131 GLU ASN VAL ASP GLU PRO THR LYS CYS PHE GLY LEU ASP SEQRES 9 A 131 VAL HIS THR GLU TYR ARG THR TRP THR ASP LEU PRO CYS SEQRES 10 A 131 GLY GLU LYS ASN PRO PHE ILE CYS LYS SER ARG LEU PRO SEQRES 11 A 131 HIS SEQRES 1 B 125 ASP GLU GLY CYS LEU PRO ASP TRP SER SER TYR LYS GLY SEQRES 2 B 125 HIS CYS TYR LYS VAL PHE LYS VAL GLU LYS THR TRP ALA SEQRES 3 B 125 ASP ALA GLU LYS PHE CYS LYS GLU LEU VAL ASN GLY GLY SEQRES 4 B 125 HIS LEU MET SER VAL ASN SER ARG GLU GLU GLY GLU PHE SEQRES 5 B 125 ILE SER LYS LEU ALA LEU GLU LYS MET ARG ILE VAL LEU SEQRES 6 B 125 VAL TRP ILE GLY LEU SER HIS PHE TRP ARG ILE CYS PRO SEQRES 7 B 125 LEU ARG TRP THR ASP GLY ALA ARG LEU ASP TYR ARG ALA SEQRES 8 B 125 LEU SER ASP GLU PRO ILE CYS PHE VAL ALA GLU SER PHE SEQRES 9 B 125 HIS ASN LYS TRP ILE GLN TRP THR CYS ASN ARG LYS LYS SEQRES 10 B 125 SER PHE VAL CYS LYS TYR ARG VAL FORMUL 3 HOH *143(H2 O) HELIX 1 1 THR A 24 ASN A 35 1 12 HELIX 2 2 SER A 44 LEU A 59 1 16 HELIX 3 3 VAL A 105 GLU A 108 5 4 HELIX 4 4 THR B 24 VAL B 36 1 13 HELIX 5 5 SER B 46 LYS B 60 1 15 HELIX 6 6 PHE B 73 CYS B 77 5 5 SHEET 1 A 4 SER A 9 TYR A 11 0 SHEET 2 A 4 HIS A 14 GLY A 23 -1 O TYR A 16 N SER A 9 SHEET 3 A 4 ASN A 121 SER A 127 -1 O PHE A 123 N PHE A 19 SHEET 4 A 4 HIS A 38 LEU A 39 -1 N HIS A 38 O LYS A 126 SHEET 1 B 4 TRP A 112 LEU A 115 0 SHEET 2 B 4 CYS A 100 LEU A 103 -1 N CYS A 100 O LEU A 115 SHEET 3 B 4 ALA A 66 ASP A 72 -1 N ALA A 66 O LEU A 103 SHEET 4 B 4 LEU B 79 TRP B 81 -1 O ARG B 80 N ARG A 71 SHEET 1 C 4 SER B 9 TYR B 11 0 SHEET 2 C 4 HIS B 14 LYS B 23 -1 O TYR B 16 N SER B 9 SHEET 3 C 4 LYS B 117 ARG B 124 -1 O PHE B 119 N PHE B 19 SHEET 4 C 4 HIS B 40 LEU B 41 -1 N HIS B 40 O LYS B 122 SHEET 1 D 6 SER B 9 TYR B 11 0 SHEET 2 D 6 HIS B 14 LYS B 23 -1 O TYR B 16 N SER B 9 SHEET 3 D 6 LYS B 117 ARG B 124 -1 O PHE B 119 N PHE B 19 SHEET 4 D 6 LEU B 65 HIS B 72 1 N TRP B 67 O SER B 118 SHEET 5 D 6 ILE B 97 GLU B 102 -1 O ILE B 97 N HIS B 72 SHEET 6 D 6 TRP B 108 THR B 112 -1 O TRP B 111 N CYS B 98 SSBOND 1 CYS A 4 CYS A 15 1555 1555 2.03 SSBOND 2 CYS A 32 CYS A 125 1555 1555 2.03 SSBOND 3 CYS A 79 CYS B 77 1555 1555 2.03 SSBOND 4 CYS A 100 CYS A 117 1555 1555 2.03 SSBOND 5 CYS B 4 CYS B 15 1555 1555 2.02 SSBOND 6 CYS B 32 CYS B 121 1555 1555 2.04 SSBOND 7 CYS B 98 CYS B 113 1555 1555 2.03 CRYST1 35.350 61.740 120.930 90.00 90.00 90.00 P 21 21 21 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 0.028289 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008269 0.00000