PDB Short entry for 1BF9 HEADER BLOOD COAGULATION 28-MAY-98 1BF9 TITLE N-TERMINAL EGF-LIKE DOMAIN FROM HUMAN FACTOR VII, NMR, 23 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: FACTOR VII; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL EGF-LIKE DOMAIN; COMPND 5 EC: 3.4.21.21; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BLOOD KEYWDS BLOOD COAGULATION, EGF, HYDROLASE, SERINE PROTEASE EXPDTA SOLUTION NMR NUMMDL 23 AUTHOR A.MURANYI,B.E.FINN,G.P.GIPPERT,S.FORSEN,J.STENFLO,T.DRAKENBERG REVDAT 3 29-NOV-17 1BF9 1 REMARK HELIX REVDAT 2 24-FEB-09 1BF9 1 VERSN REVDAT 1 16-FEB-99 1BF9 0 JRNL AUTH A.MURANYI,B.E.FINN,G.P.GIPPERT,S.FORSEN,J.STENFLO, JRNL AUTH 2 T.DRAKENBERG JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL EGF-LIKE DOMAIN FROM JRNL TITL 2 HUMAN FACTOR VII. JRNL REF BIOCHEMISTRY V. 37 10605 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9692950 JRNL DOI 10.1021/BI980522F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.W.BANNER,A.D'ARCY,C.CHENE,F.K.WINKLER,A.GUHA, REMARK 1 AUTH 2 W.H.KONIGSBERG,Y.NEMERSON,D.KIRCHHOFER REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE COMPLEX OF BLOOD COAGULATION REMARK 1 TITL 2 FACTOR VIIA WITH SOLUBLE TISSUE FACTOR REMARK 1 REF NATURE V. 380 41 1996 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.BARON,D.G.NORMAN,T.S.HARVEY,P.A.HANDFORD,M.MAYHEW,A.G.TSE, REMARK 1 AUTH 2 G.G.BROWNLEE,I.D.CAMPBELL REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF THE FIRST EGF-LIKE MODULE REMARK 1 TITL 2 OF HUMAN FACTOR IX: COMPARISON WITH EGF AND TGF-ALPHA REMARK 1 REF PROTEIN SCI. V. 1 81 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.ULLNER,M.SELANDER,E.PERSSON,J.STENFLO,T.DRAKENBERG, REMARK 1 AUTH 2 O.TELEMAN REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE APO FORM OF THE REMARK 1 TITL 2 N-TERMINAL EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X AS REMARK 1 TITL 3 DETERMINED BY NMR SPECTROSCOPY AND SIMULATED FOLDING REMARK 1 REF BIOCHEMISTRY V. 31 5974 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BF9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171685. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : NO SALT ADDED REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : H2O AND D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY; 2Q; TOCSY; NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : OMEGA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : GE; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY EMBEDDING REMARK 210 WITHOUT METRIZATION FOLLOWED BY REMARK 210 RESTRAINED SIMULATED ANNEALING REMARK 210 AND SIMULATED ANNEALING REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO DISTANCE RESTRAINT VIOLATED REMARK 210 BY MORE THAN 0.2 ANGSTROM AND NO REMARK 210 DIHEDRAL ANGLE RESTRAINTS REMARK 210 VIOLATED BY MORE THAN 2 DEGREES 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 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: 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 ASP A 46 109.49 61.74 REMARK 500 1 CYS A 50 43.70 -83.55 REMARK 500 1 SER A 53 70.49 50.91 REMARK 500 1 GLN A 64 -165.64 -103.79 REMARK 500 1 SER A 67 -112.44 179.36 REMARK 500 1 CYS A 72 179.43 -58.41 REMARK 500 1 THR A 83 76.71 -104.24 REMARK 500 2 ASP A 48 -89.63 -60.91 REMARK 500 2 GLN A 49 -58.73 -129.15 REMARK 500 2 LEU A 65 -82.03 -51.02 REMARK 500 2 GLN A 66 -31.42 -36.18 REMARK 500 2 SER A 67 -153.43 169.91 REMARK 500 2 CYS A 72 -159.53 41.13 REMARK 500 3 GLN A 49 -83.13 40.53 REMARK 500 3 CYS A 50 43.23 -80.79 REMARK 500 3 SER A 53 86.30 67.74 REMARK 500 3 CYS A 55 151.69 -42.45 REMARK 500 3 SER A 67 -134.90 179.63 REMARK 500 3 CYS A 72 -160.53 -105.43 REMARK 500 3 GLU A 77 114.82 -170.21 REMARK 500 3 ASN A 80 19.54 -152.20 REMARK 500 3 THR A 83 75.82 -118.04 REMARK 500 4 ASP A 48 -83.64 -175.07 REMARK 500 4 SER A 53 76.93 67.52 REMARK 500 4 SER A 67 -131.13 -178.96 REMARK 500 4 CYS A 72 -159.27 -74.92 REMARK 500 4 ASN A 80 27.75 -152.71 REMARK 500 4 THR A 83 67.67 -111.92 REMARK 500 5 ASP A 46 -100.75 -179.37 REMARK 500 5 ASP A 48 -82.82 -176.50 REMARK 500 5 SER A 52 18.93 -149.50 REMARK 500 5 SER A 53 72.60 54.29 REMARK 500 5 SER A 67 -123.59 179.04 REMARK 500 5 CYS A 72 177.82 -59.25 REMARK 500 5 GLU A 77 113.82 -167.22 REMARK 500 5 ASN A 80 21.89 -140.07 REMARK 500 5 CYS A 81 18.93 53.98 REMARK 500 6 ASP A 48 -99.89 -178.19 REMARK 500 6 GLN A 49 -59.03 -130.43 REMARK 500 6 CYS A 50 41.22 -81.57 REMARK 500 6 SER A 53 75.07 58.26 REMARK 500 6 GLN A 64 -165.07 -106.79 REMARK 500 6 SER A 67 -132.90 -178.17 REMARK 500 6 CYS A 72 -175.37 -56.97 REMARK 500 6 GLU A 77 -36.14 -161.67 REMARK 500 6 THR A 83 66.41 -103.97 REMARK 500 6 HIS A 84 108.13 -50.20 REMARK 500 7 ASP A 46 -40.16 -163.31 REMARK 500 7 ASP A 48 117.88 58.87 REMARK 500 7 SER A 53 77.46 58.97 REMARK 500 REMARK 500 THIS ENTRY HAS 190 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 79 0.24 SIDE CHAIN REMARK 500 2 ARG A 79 0.30 SIDE CHAIN REMARK 500 3 ARG A 79 0.31 SIDE CHAIN REMARK 500 4 ARG A 79 0.20 SIDE CHAIN REMARK 500 5 ARG A 79 0.25 SIDE CHAIN REMARK 500 6 ARG A 79 0.18 SIDE CHAIN REMARK 500 7 ARG A 79 0.23 SIDE CHAIN REMARK 500 8 ARG A 79 0.31 SIDE CHAIN REMARK 500 9 ARG A 79 0.18 SIDE CHAIN REMARK 500 10 ARG A 79 0.28 SIDE CHAIN REMARK 500 11 ARG A 79 0.29 SIDE CHAIN REMARK 500 12 ARG A 79 0.30 SIDE CHAIN REMARK 500 13 ARG A 79 0.16 SIDE CHAIN REMARK 500 14 ARG A 79 0.25 SIDE CHAIN REMARK 500 15 ARG A 79 0.32 SIDE CHAIN REMARK 500 16 ARG A 79 0.13 SIDE CHAIN REMARK 500 17 ARG A 79 0.29 SIDE CHAIN REMARK 500 18 ARG A 79 0.32 SIDE CHAIN REMARK 500 19 ARG A 79 0.29 SIDE CHAIN REMARK 500 20 ARG A 79 0.27 SIDE CHAIN REMARK 500 21 ARG A 79 0.28 SIDE CHAIN REMARK 500 22 ARG A 79 0.09 SIDE CHAIN REMARK 500 23 ARG A 79 0.31 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BF9 A 45 85 UNP P08709 FA7_HUMAN 105 145 SEQRES 1 A 41 SER ASP GLY ASP GLN CYS ALA SER SER PRO CYS GLN ASN SEQRES 2 A 41 GLY GLY SER CYS LYS ASP GLN LEU GLN SER TYR ILE CYS SEQRES 3 A 41 PHE CYS LEU PRO ALA PHE GLU GLY ARG ASN CYS GLU THR SEQRES 4 A 41 HIS LYS HELIX 1 1 ASP A 48 SER A 52 5 5 SHEET 1 S1 2 SER A 60 ASP A 63 0 SHEET 2 S1 2 TYR A 68 PHE A 71 -1 SHEET 1 S2 2 PHE A 76 GLU A 77 0 SHEET 2 S2 2 THR A 83 HIS A 84 -1 SSBOND 1 CYS A 50 CYS A 61 1555 1555 2.02 SSBOND 2 CYS A 55 CYS A 70 1555 1555 2.02 SSBOND 3 CYS A 72 CYS A 81 1555 1555 2.02 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