PDB Short entry for 1ATZ HEADER COLLAGEN-BINDING 15-AUG-97 1ATZ TITLE HUMAN VON WILLEBRAND FACTOR A3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VON WILLEBRAND FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: A3-DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: B834; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS COLLAGEN-BINDING, HEMOSTASIS, DINUCLEOTIDE BINDING FOLD EXPDTA X-RAY DIFFRACTION AUTHOR E.G.HUIZINGA,P.GROS REVDAT 3 24-FEB-09 1ATZ 1 VERSN REVDAT 2 01-APR-03 1ATZ 1 JRNL REVDAT 1 25-FEB-98 1ATZ 0 JRNL AUTH E.G.HUIZINGA,R.MARTIJN VAN DER PLAS,J.KROON, JRNL AUTH 2 J.J.SIXMA,P.GROS JRNL TITL CRYSTAL STRUCTURE OF THE A3 DOMAIN OF HUMAN VON JRNL TITL 2 WILLEBRAND FACTOR: IMPLICATIONS FOR COLLAGEN JRNL TITL 3 BINDING. JRNL REF STRUCTURE V. 5 1147 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9331419 JRNL DOI 10.1016/S0969-2126(97)00266-9 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.2 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27813 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) : 0.174 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2112 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3208 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 252 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3148 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 355 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.60 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.24 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) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ATZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : 28127 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 43.8000 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) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.05900 REMARK 200 R SYM FOR SHELL (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 29.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 1.8 A IS THE HIGH RESOLUTION LIMIT OF THE DATA USED FOR REMARK 200 REFINEMENT, NOT THE DIFFRACTION LIMIT OF THE CRYSTAL. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3000, 200 MM SODIUM REMARK 280 ACETATE, 100 MM TRIS/HCL PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 49.26000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 922 REMARK 465 CYS A 923 REMARK 465 SER A 924 REMARK 465 CYS A 1109 REMARK 465 SER A 1110 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 LEU A 964 -131.05 -119.08 REMARK 500 SER A1020 47.88 -96.65 REMARK 500 LEU B 964 -114.59 -123.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 1ATZ A 922 1110 UNP P04275 VWF_HUMAN 1685 1873 DBREF 1ATZ B 922 1110 UNP P04275 VWF_HUMAN 1685 1873 SEQRES 1 A 189 ASP CYS SER GLN PRO LEU ASP VAL ILE LEU LEU LEU ASP SEQRES 2 A 189 GLY SER SER SER PHE PRO ALA SER TYR PHE ASP GLU MET SEQRES 3 A 189 LYS SER PHE ALA LYS ALA PHE ILE SER LYS ALA ASN ILE SEQRES 4 A 189 GLY PRO ARG LEU THR GLN VAL SER VAL LEU GLN TYR GLY SEQRES 5 A 189 SER ILE THR THR ILE ASP VAL PRO TRP ASN VAL VAL PRO SEQRES 6 A 189 GLU LYS ALA HIS LEU LEU SER LEU VAL ASP VAL MET GLN SEQRES 7 A 189 ARG GLU GLY GLY PRO SER GLN ILE GLY ASP ALA LEU GLY SEQRES 8 A 189 PHE ALA VAL ARG TYR LEU THR SER GLU MET HIS GLY ALA SEQRES 9 A 189 ARG PRO GLY ALA SER LYS ALA VAL VAL ILE LEU VAL THR SEQRES 10 A 189 ASP VAL SER VAL ASP SER VAL ASP ALA ALA ALA ASP ALA SEQRES 11 A 189 ALA ARG SER ASN ARG VAL THR VAL PHE PRO ILE GLY ILE SEQRES 12 A 189 GLY ASP ARG TYR ASP ALA ALA GLN LEU ARG ILE LEU ALA SEQRES 13 A 189 GLY PRO ALA GLY ASP SER ASN VAL VAL LYS LEU GLN ARG SEQRES 14 A 189 ILE GLU ASP LEU PRO THR MET VAL THR LEU GLY ASN SER SEQRES 15 A 189 PHE LEU HIS LYS LEU CYS SER SEQRES 1 B 189 ASP CYS SER GLN PRO LEU ASP VAL ILE LEU LEU LEU ASP SEQRES 2 B 189 GLY SER SER SER PHE PRO ALA SER TYR PHE ASP GLU MET SEQRES 3 B 189 LYS SER PHE ALA LYS ALA PHE ILE SER LYS ALA ASN ILE SEQRES 4 B 189 GLY PRO ARG LEU THR GLN VAL SER VAL LEU GLN TYR GLY SEQRES 5 B 189 SER ILE THR THR ILE ASP VAL PRO TRP ASN VAL VAL PRO SEQRES 6 B 189 GLU LYS ALA HIS LEU LEU SER LEU VAL ASP VAL MET GLN SEQRES 7 B 189 ARG GLU GLY GLY PRO SER GLN ILE GLY ASP ALA LEU GLY SEQRES 8 B 189 PHE ALA VAL ARG TYR LEU THR SER GLU MET HIS GLY ALA SEQRES 9 B 189 ARG PRO GLY ALA SER LYS ALA VAL VAL ILE LEU VAL THR SEQRES 10 B 189 ASP VAL SER VAL ASP SER VAL ASP ALA ALA ALA ASP ALA SEQRES 11 B 189 ALA ARG SER ASN ARG VAL THR VAL PHE PRO ILE GLY ILE SEQRES 12 B 189 GLY ASP ARG TYR ASP ALA ALA GLN LEU ARG ILE LEU ALA SEQRES 13 B 189 GLY PRO ALA GLY ASP SER ASN VAL VAL LYS LEU GLN ARG SEQRES 14 B 189 ILE GLU ASP LEU PRO THR MET VAL THR LEU GLY ASN SER SEQRES 15 B 189 PHE LEU HIS LYS LEU CYS SER FORMUL 3 HOH *350(H2 O) HELIX 1 1 ALA A 941 LYS A 957 1 17 HELIX 2 2 LYS A 988 ASP A 996 1 9 HELIX 3 3 ILE A 1007 THR A 1019 1 13 HELIX 4 4 ASP A 1046 SER A 1054 1 9 HELIX 5 5 ALA A 1070 LEU A 1076 1 7 HELIX 6 6 ASP A 1093 THR A 1099 1IRREGULAR DUE TO PRO A 1095 7 HELIX 7 7 SER A 1103 HIS A 1106 1 4 HELIX 8 8 ALA B 941 LYS B 957 1 17 HELIX 9 9 LYS B 988 ASP B 996 1 9 HELIX 10 10 ILE B 1007 THR B 1019 1 13 HELIX 11 11 ASP B 1046 ASN B 1055 1 10 HELIX 12 12 ALA B 1070 LEU B 1076 1 7 HELIX 13 13 ASP B 1093 THR B 1099 1IRREGULAR DUE TO PRO B 1095 7 HELIX 14 14 SER B 1103 LEU B 1108 1 6 SHEET 1 A 6 VAL A1086 LEU A1088 0 SHEET 2 A 6 VAL A1057 ILE A1064 1 N GLY A1063 O VAL A1086 SHEET 3 A 6 SER A1030 VAL A1037 1 N LYS A1031 O THR A1058 SHEET 4 A 6 LEU A 927 ASP A 934 1 N ASP A 928 O SER A1030 SHEET 5 A 6 THR A 965 TYR A 972 1 N GLN A 966 O LEU A 927 SHEET 6 A 6 THR A 976 VAL A 980 -1 N VAL A 980 O VAL A 969 SHEET 1 B 6 VAL B1086 LEU B1088 0 SHEET 2 B 6 VAL B1057 ILE B1064 1 N GLY B1063 O VAL B1086 SHEET 3 B 6 SER B1030 VAL B1037 1 N LYS B1031 O THR B1058 SHEET 4 B 6 LEU B 927 ASP B 934 1 N ASP B 928 O SER B1030 SHEET 5 B 6 THR B 965 TYR B 972 1 N GLN B 966 O LEU B 927 SHEET 6 B 6 THR B 976 VAL B 980 -1 N VAL B 980 O VAL B 969 SSBOND 1 CYS B 923 CYS B 1109 1555 1555 2.03 CRYST1 35.200 98.520 44.580 90.00 90.64 90.00 P 1 21 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 0.028409 0.000000 0.000317 0.00000 SCALE2 0.000000 0.010150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022433 0.00000 MTRIX1 1 0.999455 0.028447 -0.016722 -18.48800 1 MTRIX2 1 0.028656 -0.999512 0.012388 48.60970 1 MTRIX3 1 -0.016362 -0.012861 -0.999783 67.04930 1