PDB Short entry for 1IJB HEADER BLOOD CLOTTING 25-APR-01 1IJB TITLE THE VON WILLEBRAND FACTOR MUTANT (I546V) A1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VON WILLEBRAND FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: A1 DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DINUCLEOTIDE-BINDING FOLD, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR K.FUKUDA,T.A.DOGGETT,L.A.BANKSTON,M.A.CRUZ,T.G.DIACOVO,R.C.LIDDINGTON REVDAT 6 16-AUG-23 1IJB 1 REMARK REVDAT 5 27-OCT-21 1IJB 1 SEQADV REVDAT 4 24-FEB-09 1IJB 1 VERSN REVDAT 3 01-APR-03 1IJB 1 JRNL REVDAT 2 17-JUL-02 1IJB 1 TITLE JRNL REVDAT 1 10-JUL-02 1IJB 0 JRNL AUTH K.FUKUDA,T.A.DOGGETT,L.A.BANKSTON,M.A.CRUZ,T.G.DIACOVO, JRNL AUTH 2 R.C.LIDDINGTON JRNL TITL STRUCTURAL BASIS OF VON WILLEBRAND FACTOR ACTIVATION BY THE JRNL TITL 2 SNAKE TOXIN BOTROCETIN. JRNL REF STRUCTURE V. 10 943 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12121649 JRNL DOI 10.1016/S0969-2126(02)00787-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A1 DOMAIN AND REMARK 1 TITL 2 IMPLICATIONS FOR THE BINDING OF PLATELET GLYCOPROTEIN IB REMARK 1 REF J.BIOL.CHEM. V. 273 10396 1998 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 617771.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 24004 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) : 0.188 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1154 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3316 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 177 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1620 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.50000 REMARK 3 B22 (A**2) : 2.50000 REMARK 3 B33 (A**2) : -4.99000 REMARK 3 B12 (A**2) : 1.11000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.190 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.190 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.72 REMARK 3 BSOL : 86.11 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 96 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25460 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.9000 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) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 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 1AUQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, AMMONIUM REMARK 280 ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 22.83400 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 45.66800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.25100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.08500 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 11.41700 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 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 ARG A 571 CG CD NE CZ NH1 NH2 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 SER A 510 69.95 -115.58 REMARK 500 TRP A 550 -105.74 -129.31 REMARK 500 HIS A 559 -132.98 -135.23 REMARK 500 ASN A 672 91.27 -69.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AUQ RELATED DB: PDB REMARK 900 1AUQ IS THE WILD TYPE A1 DOMAIN REMARK 900 RELATED ID: 1IJK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BIMOLECULAR COMPLEX OF THE VON WILLEBRAND REMARK 900 FACTOR A1 DOMAIN-BOTROCETIN DBREF 1IJB A 500 701 UNP P04275 VWF_HUMAN 1263 1464 SEQADV 1IJB VAL A 546 UNP P04275 ILE 1309 ENGINEERED MUTATION SEQRES 1 A 202 SER GLU PRO PRO LEU HIS ASP PHE TYR CYS SER ARG LEU SEQRES 2 A 202 LEU ASP LEU VAL PHE LEU LEU ASP GLY SER SER ARG LEU SEQRES 3 A 202 SER GLU ALA GLU PHE GLU VAL LEU LYS ALA PHE VAL VAL SEQRES 4 A 202 ASP MET MET GLU ARG LEU ARG VAL SER GLN LYS TRP VAL SEQRES 5 A 202 ARG VAL ALA VAL VAL GLU TYR HIS ASP GLY SER HIS ALA SEQRES 6 A 202 TYR ILE GLY LEU LYS ASP ARG LYS ARG PRO SER GLU LEU SEQRES 7 A 202 ARG ARG ILE ALA SER GLN VAL LYS TYR ALA GLY SER GLN SEQRES 8 A 202 VAL ALA SER THR SER GLU VAL LEU LYS TYR THR LEU PHE SEQRES 9 A 202 GLN ILE PHE SER LYS ILE ASP ARG PRO GLU ALA SER ARG SEQRES 10 A 202 ILE ALA LEU LEU LEU MET ALA SER GLN GLU PRO GLN ARG SEQRES 11 A 202 MET SER ARG ASN PHE VAL ARG TYR VAL GLN GLY LEU LYS SEQRES 12 A 202 LYS LYS LYS VAL ILE VAL ILE PRO VAL GLY ILE GLY PRO SEQRES 13 A 202 HIS ALA ASN LEU LYS GLN ILE ARG LEU ILE GLU LYS GLN SEQRES 14 A 202 ALA PRO GLU ASN LYS ALA PHE VAL LEU SER SER VAL ASP SEQRES 15 A 202 GLU LEU GLU GLN GLN ARG ASP GLU ILE VAL SER TYR LEU SEQRES 16 A 202 CYS ASP LEU ALA PRO GLU ALA FORMUL 2 HOH *233(H2 O) HELIX 1 1 SER A 526 ARG A 543 1 18 HELIX 2 2 ARG A 573 GLN A 583 1 11 HELIX 3 3 SER A 593 ILE A 605 1 13 HELIX 4 4 PRO A 627 SER A 631 5 5 HELIX 5 5 ASN A 633 LYS A 644 1 12 HELIX 6 6 ASN A 658 ALA A 669 1 12 HELIX 7 7 SER A 679 ASP A 681 5 3 HELIX 8 8 GLU A 682 ALA A 698 1 17 SHEET 1 A 6 SER A 562 ILE A 566 0 SHEET 2 A 6 VAL A 551 TYR A 558 -1 O VAL A 555 N TYR A 565 SHEET 3 A 6 LEU A 513 ASP A 520 1 O LEU A 513 N ARG A 552 SHEET 4 A 6 SER A 615 MET A 622 1 O SER A 615 N ASP A 514 SHEET 5 A 6 VAL A 646 ILE A 653 1 N ILE A 647 O ARG A 616 SHEET 6 A 6 PHE A 675 LEU A 677 1 N PHE A 675 O PRO A 650 SSBOND 1 CYS A 509 CYS A 695 1555 1555 2.04 CRYST1 86.010 86.010 68.502 90.00 90.00 120.00 P 61 6 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 0.011627 0.006713 0.000000 0.00000 SCALE2 0.000000 0.013425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014598 0.00000