HEADER BLOOD CLOTTING 21-MAY-09 2KJ4 TITLE SOLUTION STRUCTURE OF THE COMPLEX OF VEK-30 AND PLASMINOGEN TITLE 2 KRINGLE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMINOGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VEK-30; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: FRAGMENT OF M PROTEIN, RESIDUES 85-113; COMPND 9 ENGINEERED: 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: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PPIC9K; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 10 ORGANISM_TAXID: 1314; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_VECTOR: PET-15B KEYWDS PROTEIN/PEPTIDE, BLOOD CLOTTING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.WANG,J.ZAJICEK,M.PROROK,F.J.CASTELLIN REVDAT 2 09-MAR-10 2KJ4 1 JRNL REVDAT 1 20-OCT-09 2KJ4 0 JRNL AUTH M.WANG,J.ZAJICEK,J.H.GEIGER,M.PROROK,F.J.CASTELLINO JRNL TITL SOLUTION STRUCTURE OF THE COMPLEX OF VEK-30 AND JRNL TITL 2 PLASMINOGEN KRINGLE 2. JRNL REF J.STRUCT.BIOL. V. 169 349 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 19800007 JRNL DOI 10.1016/J.JSB.2009.09.011 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS, RECOORD REMARK 4 REMARK 4 2KJ4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-09. REMARK 100 THE RCSB ID CODE IS RCSB101183. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] REMARK 210 PLASMINOGEN, 1 MM VEK-30, 50 REMARK 210 MM [U-100% 2H] HEPES, 200 MM REMARK 210 SODIUM CHLORIDE, 3 MM SODIUM REMARK 210 AZIDE, 0.2 MM DSS, 90% H2O/10% REMARK 210 D2O; 1 MM PLASMINOGEN, 1 MM [U REMARK 210 -15N] VEK-30, 50 MM [U-100% REMARK 210 2H] HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 3 MM SODIUM AZIDE, REMARK 210 0.2 MM DSS-12, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY; 2D 1H- REMARK 210 1H TOCSY; 3D CBCA(CO)NH; 3D REMARK 210 HNCA; 3D HNCO; 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1, NMRPIPE, NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 : 1 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 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 HH12 ARG A 62 OD2 ASP B 107 1.59 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 GLU A 6 138.00 72.46 REMARK 500 1 LYS A 54 -145.20 48.86 REMARK 500 1 ARG A 62 60.44 65.25 REMARK 500 1 PRO A 83 167.97 -49.87 REMARK 500 1 VAL B 101 31.64 -83.49 REMARK 500 2 GLU A 6 112.24 83.10 REMARK 500 2 GLU A 7 -78.19 -75.93 REMARK 500 2 LYS A 54 -134.36 51.53 REMARK 500 2 ARG A 62 57.86 70.26 REMARK 500 2 SER B 100 41.34 -152.16 REMARK 500 2 SER B 128 -76.14 64.55 REMARK 500 3 PHE A 4 71.47 -155.84 REMARK 500 3 SER A 5 -77.27 -107.80 REMARK 500 3 CYS A 8 -169.11 -163.27 REMARK 500 3 TYR A 42 76.31 -100.92 REMARK 500 3 PHE A 47 75.50 -119.70 REMARK 500 3 LYS A 54 -110.79 37.12 REMARK 500 3 ASP A 63 -171.67 -63.34 REMARK 500 3 GLU B 102 -95.23 -77.63 REMARK 500 3 LYS B 103 79.62 163.37 REMARK 500 3 LEU B 104 -76.36 69.60 REMARK 500 4 VAL A 2 89.95 50.91 REMARK 500 4 GLU A 7 91.69 65.42 REMARK 500 4 LYS A 54 -136.24 46.16 REMARK 500 4 ARG A 62 60.32 76.43 REMARK 500 4 PRO A 83 162.98 -49.41 REMARK 500 4 VAL B 101 -54.33 70.91 REMARK 500 4 GLU B 102 -135.33 -121.76 REMARK 500 4 LEU B 104 -42.64 74.77 REMARK 500 4 SER B 128 147.44 75.93 REMARK 500 5 LYS A 19 67.48 -107.47 REMARK 500 5 LYS A 54 -113.72 43.24 REMARK 500 5 ASP A 63 170.54 -59.68 REMARK 500 5 VAL B 101 30.92 -88.63 REMARK 500 5 LYS B 103 -22.64 153.16 REMARK 500 5 LEU B 104 76.03 77.38 REMARK 500 5 THR B 105 147.17 166.29 REMARK 500 6 GLU A 3 -65.39 66.52 REMARK 500 6 GLU A 6 163.75 175.60 REMARK 500 6 GLU A 7 -43.22 70.95 REMARK 500 6 TYR A 42 77.76 -101.09 REMARK 500 6 LYS A 54 -134.66 48.45 REMARK 500 6 ARG A 62 34.51 77.08 REMARK 500 6 ALA A 86 41.52 -97.03 REMARK 500 6 GLU B 102 -44.72 -145.32 REMARK 500 6 LYS B 103 43.91 73.02 REMARK 500 6 LEU B 104 77.46 66.98 REMARK 500 6 THR B 105 127.35 72.75 REMARK 500 7 LYS A 54 -133.50 37.47 REMARK 500 7 ARG A 62 60.05 64.07 REMARK 500 REMARK 500 THIS ENTRY HAS 142 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 6 ARG A 62 0.09 SIDE CHAIN REMARK 500 8 ARG A 76 0.07 SIDE CHAIN REMARK 500 14 ARG A 58 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ATOM NUMBERING IN THE PDB FILE DIFFERS FROM THAT IN THE REMARK 999 CITATION. THE NUMBERING IN THE CITATION IS AS FOLLOWS. CHAIN A: REMARK 999 TYR(-7) - ALA(80); CHAIN B: GLY(-2) - TYR(30) DBREF 2KJ4 B 101 129 UNP Q6V4L8 Q6V4L8_STRPY 85 113 DBREF 2KJ4 A 1 87 PDB 2KJ4 2KJ4 1 87 SEQADV 2KJ4 GLY B 99 UNP Q6V4L8 EXPRESSION TAG SEQADV 2KJ4 SER B 100 UNP Q6V4L8 EXPRESSION TAG SEQADV 2KJ4 TYR B 130 UNP Q6V4L8 INSERTION SEQRES 1 A 87 TYR VAL GLU PHE SER GLU GLU CYS MET HIS GLY SER GLY SEQRES 2 A 87 GLU ASN TYR ASP GLY LYS ILE SER LYS THR MET SER GLY SEQRES 3 A 87 LEU GLU CYS GLN ALA TRP ASP SER GLN SER PRO HIS ALA SEQRES 4 A 87 HIS GLY TYR ILE PRO SER LYS PHE PRO ASN LYS ASN LEU SEQRES 5 A 87 LYS LYS ASN TYR CYS ARG ASN PRO ASP ARG ASP LEU ARG SEQRES 6 A 87 PRO TRP CYS PHE THR THR ASP PRO ASN LYS ARG TRP GLU SEQRES 7 A 87 TYR CYS ASP ILE PRO ARG CYS ALA ALA SEQRES 1 B 32 GLY SER VAL GLU LYS LEU THR ALA ASP ALA GLU LEU GLN SEQRES 2 B 32 ARG LEU LYS ASN GLU ARG HIS GLU GLU ALA GLU LEU GLU SEQRES 3 B 32 ARG LEU LYS SER GLU TYR HELIX 1 1 PHE A 47 ASN A 51 5 5 HELIX 2 2 THR B 105 SER B 128 1 24 SHEET 1 A 3 CYS A 29 GLN A 30 0 SHEET 2 A 3 TRP A 67 THR A 70 -1 O PHE A 69 N GLN A 30 SHEET 3 A 3 TRP A 77 TYR A 79 -1 O GLU A 78 N CYS A 68 SSBOND 1 CYS A 8 CYS A 85 1555 1555 2.02 SSBOND 2 CYS A 29 CYS A 68 1555 1555 2.00 SSBOND 3 CYS A 57 CYS A 80 1555 1555 2.02 CISPEP 1 SER A 36 PRO A 37 1 -0.07 CISPEP 2 SER A 36 PRO A 37 2 25.72 CISPEP 3 SER A 36 PRO A 37 3 15.53 CISPEP 4 SER A 36 PRO A 37 4 12.31 CISPEP 5 SER A 36 PRO A 37 5 6.52 CISPEP 6 SER A 36 PRO A 37 6 17.35 CISPEP 7 SER A 36 PRO A 37 7 11.48 CISPEP 8 SER A 36 PRO A 37 8 12.37 CISPEP 9 SER A 36 PRO A 37 9 4.64 CISPEP 10 SER A 36 PRO A 37 10 11.07 CISPEP 11 SER A 36 PRO A 37 11 7.46 CISPEP 12 SER A 36 PRO A 37 12 18.94 CISPEP 13 SER A 36 PRO A 37 13 17.84 CISPEP 14 SER A 36 PRO A 37 14 7.39 CISPEP 15 SER A 36 PRO A 37 15 21.13 CISPEP 16 SER A 36 PRO A 37 16 10.40 CISPEP 17 SER A 36 PRO A 37 17 -17.74 CISPEP 18 SER A 36 PRO A 37 18 13.98 CISPEP 19 SER A 36 PRO A 37 19 7.67 CISPEP 20 SER A 36 PRO A 37 20 1.77 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 160 0 0 2 3 0 0 6 0 0 0 10 END