HEADER BLOOD CLOTTING 06-MAR-18 6FWN TITLE STRUCTURE AND DYNAMICS OF THE PLATELET INTEGRIN-BINDING C4 DOMAIN OF TITLE 2 VON WILLEBRAND FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VON WILLEBRAND FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VWF; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST FOUR RESIDUES IN THAT SEQUENCE (GSMA) REMAIN COMPND 7 FROM THE THROMBIN CLEAVAGE SITE AND ARE NOT PART OF THE NATIVE COMPND 8 SEQUENCE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: EXTRACELLULAR; SOURCE 6 ORGAN: BLOOD; SOURCE 7 GENE: VWF, F8VWF; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHAT3 KEYWDS VON WILLEBRAND FACTOR, VWC DOMAIN, BLOOD CLOTTING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.-R.XU,S.VON BUELOW,P.-C.CHEN,P.J.LENTING,K.KOLSEK,C.APONTE- AUTHOR 2 SANTAMARIA,B.SIMON,J.FOOT,T.OBSER,F.GRAETER,R.SCHNEPPENHEIM, AUTHOR 3 C.V.DENIS,M.WILMANNS,J.HENNIG REVDAT 3 08-MAY-19 6FWN 1 REMARK REVDAT 2 06-FEB-19 6FWN 1 JRNL REVDAT 1 24-OCT-18 6FWN 0 JRNL AUTH E.R.XU,S.VON BULOW,P.C.CHEN,P.J.LENTING,K.KOLSEK, JRNL AUTH 2 C.APONTE-SANTAMARIA,B.SIMON,J.FOOT,T.OBSER,R.SCHNEPPENHEIM, JRNL AUTH 3 F.GRATER,C.V.DENIS,M.WILMANNS,J.HENNIG JRNL TITL STRUCTURE AND DYNAMICS OF THE PLATELET INTEGRIN-BINDING C4 JRNL TITL 2 DOMAIN OF VON WILLEBRAND FACTOR. JRNL REF BLOOD V. 133 366 2019 JRNL REFN ESSN 1528-0020 JRNL PMID 30305279 JRNL DOI 10.1182/BLOOD-2018-04-843615 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT REMARK 4 REMARK 4 6FWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200008964. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.04 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 500 UM [U-13C; U-15N] VON REMARK 210 WILLEBRAND FACTOR C4 DOMAIN, 20 REMARK 210 MM SODIUM PHOSPHATE, 49.5 M H2O, REMARK 210 5.5 M D2O, 0.02 % W/V SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 500 UM REMARK 210 [U-13C; U-15N] VON WILLEBRAND REMARK 210 FACTOR C4 DOMAIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 55 M D2O, 5 MM H2O, REMARK 210 0.02 % W/V SODIUM AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-13C HMQC; 3D REMARK 210 HNCA; 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY-HSQC; 3D REMARK 210 1H-13C NOESY-HSQC; 3D 1H-13C REMARK 210 HMQC-NOESY; 3D 1H-13C HMQC-NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCEIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, NMRPIPE, TOPSPIN, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 1 PRO A2527 -179.26 -56.33 REMARK 500 1 LYS A2537 -90.04 45.90 REMARK 500 1 SER A2573 111.51 -160.46 REMARK 500 2 PRO A2506 44.55 -69.51 REMARK 500 2 PRO A2527 174.97 -59.71 REMARK 500 2 LYS A2537 -82.95 49.43 REMARK 500 2 CYS A2571 109.41 -172.77 REMARK 500 3 SER A2497 19.18 -141.48 REMARK 500 3 PRO A2506 29.93 -68.29 REMARK 500 3 ASP A2509 41.11 -83.81 REMARK 500 3 ASN A2526 -175.88 -63.92 REMARK 500 3 PRO A2527 174.53 -59.16 REMARK 500 3 LYS A2537 -94.37 45.30 REMARK 500 3 CYS A2571 140.71 -173.37 REMARK 500 4 PRO A2506 29.88 -70.79 REMARK 500 4 SER A2512 98.25 -69.03 REMARK 500 4 PRO A2527 179.93 -57.14 REMARK 500 4 LYS A2537 -100.95 50.19 REMARK 500 4 PRO A2550 -179.64 -69.33 REMARK 500 4 CYS A2571 119.89 -172.57 REMARK 500 5 PRO A2506 74.78 -65.15 REMARK 500 5 SER A2512 109.04 -56.27 REMARK 500 5 CYS A2571 138.91 -172.68 REMARK 500 6 PRO A2527 -178.93 -56.45 REMARK 500 6 LYS A2537 -101.50 40.04 REMARK 500 6 CYS A2571 143.37 -172.94 REMARK 500 7 PRO A2506 22.48 -72.57 REMARK 500 7 PRO A2527 178.06 -58.28 REMARK 500 7 CYS A2571 146.35 -176.11 REMARK 500 8 PRO A2506 22.55 -78.54 REMARK 500 8 PRO A2527 179.10 -58.14 REMARK 500 8 LYS A2537 -74.45 -27.62 REMARK 500 8 PRO A2550 -179.88 -65.67 REMARK 500 8 CYS A2571 114.18 -171.40 REMARK 500 9 SER A2494 -166.65 -119.94 REMARK 500 9 LYS A2537 -90.31 48.64 REMARK 500 9 CYS A2571 119.54 -171.52 REMARK 500 10 PRO A2506 54.79 -65.44 REMARK 500 10 PRO A2527 175.47 -54.06 REMARK 500 10 LYS A2537 -83.80 50.18 REMARK 500 10 CYS A2571 99.57 -173.47 REMARK 500 11 PRO A2527 178.68 -57.32 REMARK 500 11 LYS A2537 -94.59 44.94 REMARK 500 11 CYS A2571 106.41 -168.79 REMARK 500 12 SER A2497 18.54 -140.81 REMARK 500 12 PRO A2527 -178.98 -55.80 REMARK 500 12 LYS A2537 -98.12 48.06 REMARK 500 12 CYS A2571 108.88 -172.49 REMARK 500 13 SER A2494 -53.22 72.52 REMARK 500 13 PRO A2527 175.35 -55.87 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34243 RELATED DB: BMRB REMARK 900 STRUCTURE AND DYNAMICS OF THE PLATELET INTEGRIN-BINDING C4 DOMAIN REMARK 900 OF VON WILLEBRAND FACTOR DBREF 6FWN A 2497 2577 UNP P04275 VWF_HUMAN 2497 2577 SEQADV 6FWN GLY A 2493 UNP P04275 EXPRESSION TAG SEQADV 6FWN SER A 2494 UNP P04275 EXPRESSION TAG SEQADV 6FWN MET A 2495 UNP P04275 EXPRESSION TAG SEQADV 6FWN ALA A 2496 UNP P04275 EXPRESSION TAG SEQRES 1 A 85 GLY SER MET ALA SER ALA CYS GLU VAL VAL THR GLY SER SEQRES 2 A 85 PRO ARG GLY ASP SER GLN SER SER TRP LYS SER VAL GLY SEQRES 3 A 85 SER GLN TRP ALA SER PRO GLU ASN PRO CYS LEU ILE ASN SEQRES 4 A 85 GLU CYS VAL ARG VAL LYS GLU GLU VAL PHE ILE GLN GLN SEQRES 5 A 85 ARG ASN VAL SER CYS PRO GLN LEU GLU VAL PRO VAL CYS SEQRES 6 A 85 PRO SER GLY PHE GLN LEU SER CYS LYS THR SER ALA CYS SEQRES 7 A 85 CYS PRO SER CYS ARG CYS GLU SHEET 1 AA1 2 ALA A2498 THR A2503 0 SHEET 2 AA1 2 GLN A2511 SER A2516 -1 O LYS A2515 N CYS A2499 SHEET 1 AA2 3 GLN A2520 ALA A2522 0 SHEET 2 AA2 3 LEU A2529 VAL A2536 -1 O ASN A2531 N TRP A2521 SHEET 3 AA2 3 GLU A2539 ASN A2546 -1 O GLU A2539 N VAL A2536 SHEET 1 AA3 2 GLN A2562 CYS A2565 0 SHEET 2 AA3 2 CYS A2574 GLU A2577 -1 O ARG A2575 N SER A2564 SSBOND 1 CYS A 2499 CYS A 2533 1555 1555 2.03 SSBOND 2 CYS A 2528 CYS A 2570 1555 1555 2.04 SSBOND 3 CYS A 2549 CYS A 2571 1555 1555 2.03 SSBOND 4 CYS A 2557 CYS A 2576 1555 1555 2.03 SSBOND 5 CYS A 2565 CYS A 2574 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1