HEADER BLOOD CLOTTING 21-MAY-09 2KJ4 TITLE SOLUTION STRUCTURE OF THE COMPLEX OF VEK-30 AND PLASMINOGEN 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 3 16-MAR-22 2KJ4 1 REMARK SEQADV 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 PLASMINOGEN JRNL TITL 2 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, CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS, RECOORD REMARK 4 REMARK 4 2KJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101183. 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] PLASMINOGEN, REMARK 210 1 MM VEK-30, 50 MM [U-100% 2H] REMARK 210 HEPES, 200 MM SODIUM CHLORIDE, 3 REMARK 210 MM SODIUM AZIDE, 0.2 MM DSS, 90% REMARK 210 H2O/10% D2O; 1 MM PLASMINOGEN, 1 REMARK 210 MM [U-15N] VEK-30, 50 MM [U-100% REMARK 210 2H] HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 3 MM SODIUM AZIDE, 0.2 REMARK 210 MM DSS-12, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-1H TOCSY; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D HNCO; REMARK 210 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 : NMRPIPE, NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MODEL 1