PDB Short entry for 2JPQ HEADER STRUCTURAL GENOMICS 21-MAY-07 2JPQ TITLE SOLUTION NMR STRUCTURE OF HOMODIMER VP2129 FROM VIBRIO TITLE 2 PARAHAEMOLYTICUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 VPR61. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0352 PROTEIN VP2129; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 670; SOURCE 4 GENE: VP2129; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PMGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS DIMER, ALL ALPHA, HOMODIMER, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,J.R.CORT,H.WANG,C.NWOSU,K.CUNNINGHAM,L.OWENS,L.-C.MA, AUTHOR 2 R.XIAO,J.LIU,M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 7 08-MAY-24 2JPQ 1 REMARK REVDAT 6 20-DEC-23 2JPQ 1 REMARK REVDAT 5 14-JUN-23 2JPQ 1 REMARK REVDAT 4 19-FEB-20 2JPQ 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JPQ 1 VERSN REVDAT 2 14-AUG-07 2JPQ 1 TITLE REVDAT 1 19-JUN-07 2JPQ 0 JRNL AUTH T.A.RAMELOT,J.R.CORT,G.A.MONTELIONE,M.A.KENNEDY JRNL TITL SOLUTION NMR STRUCTURE OF VIBRIO PARAHAEMOLYTICUS VP2129. JRNL TITL 2 NORTHEAST STRUCTURAL GENOMICS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE NMRPIPE_LINUX, CNS 1.1 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JPQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000100134. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4 MM [U-13C; U-15N] VP2129, REMARK 210 100 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 20 MM AMMONIUM REMARK 210 ACETATE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O; REMARK 210 1.4 MM [U-5% 13C; U-100% 15N] REMARK 210 VP2129, 100 MM SODIUM CHLORIDE, REMARK 210 5 MM CALCIUM CHLORIDE, 20 MM REMARK 210 AMMONIUM ACETATE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 95% H2O/5% REMARK 210 D2O; 1.4 MM [U-13C; U-15N] REMARK 210 VP2129, 100 MM SODIUM CHLORIDE, REMARK 210 5 MM CALCIUM CHLORIDE, 20 MM REMARK 210 AMMONIUM ACETATE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 100% D2O; REMARK 210 0.4 MM [U-13C; U-15N] VP2129, REMARK 210 100 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 20 MM AMMONIUM REMARK 210 ACETATE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 0.4 MM VP2129, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPH; 3D HNCACB; 4D 1H-13C REMARK 210 NOESY; 3D HBHA(CO)NH; 3D HNHA; REMARK 210 3D CBCA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HNCO; 3D C(CO)NH; 3D HCCH-COSY; REMARK 210 3D HCCH-TOCSY; 3D EDITED REMARK 210 FILTERED 1H-13C NOESY; 3D 1H-13C REMARK 210 NOESY AROM REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, AUTOSTRUCTURE 2.1.1, X REMARK 210 -PLOR NIH 2.15.0, SPARKY 3.1, REMARK 210 AUTOASSIGN 2.3.0, CNS 1.1, PSVS REMARK 210 1.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 OE2 GLU A 18 HE2 HIS B 26 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 THR A 4 -31.43 73.85 REMARK 500 1 SER A 5 -95.84 -78.24 REMARK 500 1 LYS A 6 -13.33 69.27 REMARK 500 1 PRO A 72 104.94 -56.38 REMARK 500 1 THR A 74 88.59 60.98 REMARK 500 1 PRO B 2 45.27 -83.06 REMARK 500 1 GLN B 47 31.05 -145.57 REMARK 500 1 ARG B 48 -46.47 -155.61 REMARK 500 1 PRO B 72 45.04 -69.75 REMARK 500 1 LEU B 76 79.05 56.54 REMARK 500 1 HIS B 80 43.38 -89.30 REMARK 500 2 THR A 4 75.26 69.28 REMARK 500 2 ARG A 48 33.00 -79.87 REMARK 500 2 SER B 5 76.58 -102.41 REMARK 500 2 ARG B 48 14.10 91.62 REMARK 500 2 LYS B 73 -157.08 64.21 REMARK 500 2 THR B 74 -70.15 -74.60 REMARK 500 2 HIS B 75 -40.65 -152.32 REMARK 500 2 HIS B 78 -36.68 75.93 REMARK 500 2 HIS B 79 95.99 61.51 REMARK 500 2 HIS B 80 103.01 -166.05 REMARK 500 2 HIS B 81 134.67 -170.33 REMARK 500 3 TYR A 7 -156.60 57.30 REMARK 500 3 GLN A 47 -49.15 -130.63 REMARK 500 3 ARG A 48 40.15 -86.89 REMARK 500 3 LYS A 73 -179.06 66.78 REMARK 500 3 LEU A 76 96.15 67.42 REMARK 500 3 GLU A 77 155.47 72.77 REMARK 500 3 HIS A 79 82.81 -154.76 REMARK 500 3 HIS A 80 38.16 -81.91 REMARK 500 3 THR B 4 -167.19 -75.29 REMARK 500 3 HIS B 75 -36.06 179.23 REMARK 500 3 HIS B 81 -75.20 64.48 REMARK 500 3 HIS B 82 9.84 -161.36 REMARK 500 4 PRO A 2 34.48 -86.41 REMARK 500 4 ILE A 3 -88.56 -79.08 REMARK 500 4 TYR A 7 -154.73 56.95 REMARK 500 4 GLU A 70 -69.38 67.58 REMARK 500 4 THR A 71 91.58 62.93 REMARK 500 4 PRO A 72 84.39 -68.58 REMARK 500 4 GLU A 77 -101.15 -98.53 REMARK 500 4 HIS A 78 -43.19 66.30 REMARK 500 4 HIS A 82 112.85 70.18 REMARK 500 4 THR B 4 90.09 69.93 REMARK 500 4 TYR B 7 159.58 -48.70 REMARK 500 4 ASN B 46 -61.97 -99.47 REMARK 500 4 PRO B 72 35.70 -74.15 REMARK 500 4 THR B 74 77.67 44.00 REMARK 500 4 LEU B 76 77.08 57.68 REMARK 500 5 THR A 4 -40.27 74.11 REMARK 500 REMARK 500 THIS ENTRY HAS 215 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15258 RELATED DB: BMRB REMARK 900 RELATED ID: VPR61 RELATED DB: TARGETDB DBREF 2JPQ A 1 75 UNP Q87MV2 Y2129_VIBPA 1 75 DBREF 2JPQ B 1 75 UNP Q87MV2 Y2129_VIBPA 1 75 SEQADV 2JPQ LEU A 76 UNP Q87MV2 CLONING ARTIFACT SEQADV 2JPQ GLU A 77 UNP Q87MV2 CLONING ARTIFACT SEQADV 2JPQ HIS A 78 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS A 79 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS A 80 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS A 81 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS A 82 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS A 83 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ LEU B 76 UNP Q87MV2 CLONING ARTIFACT SEQADV 2JPQ GLU B 77 UNP Q87MV2 CLONING ARTIFACT SEQADV 2JPQ HIS B 78 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS B 79 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS B 80 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS B 81 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS B 82 UNP Q87MV2 EXPRESSION TAG SEQADV 2JPQ HIS B 83 UNP Q87MV2 EXPRESSION TAG SEQRES 1 A 83 MET PRO ILE THR SER LYS TYR THR ASP GLU GLN VAL GLU SEQRES 2 A 83 LYS ILE LEU ALA GLU VAL ALA LEU VAL LEU GLU LYS HIS SEQRES 3 A 83 ALA ALA SER PRO GLU LEU THR LEU MET ILE ALA GLY ASN SEQRES 4 A 83 ILE ALA THR ASN VAL LEU ASN GLN ARG VAL ALA ALA SER SEQRES 5 A 83 GLN ARG LYS LEU ILE ALA GLU LYS PHE ALA GLN ALA LEU SEQRES 6 A 83 MET SER SER LEU GLU THR PRO LYS THR HIS LEU GLU HIS SEQRES 7 A 83 HIS HIS HIS HIS HIS SEQRES 1 B 83 MET PRO ILE THR SER LYS TYR THR ASP GLU GLN VAL GLU SEQRES 2 B 83 LYS ILE LEU ALA GLU VAL ALA LEU VAL LEU GLU LYS HIS SEQRES 3 B 83 ALA ALA SER PRO GLU LEU THR LEU MET ILE ALA GLY ASN SEQRES 4 B 83 ILE ALA THR ASN VAL LEU ASN GLN ARG VAL ALA ALA SER SEQRES 5 B 83 GLN ARG LYS LEU ILE ALA GLU LYS PHE ALA GLN ALA LEU SEQRES 6 B 83 MET SER SER LEU GLU THR PRO LYS THR HIS LEU GLU HIS SEQRES 7 B 83 HIS HIS HIS HIS HIS HELIX 1 1 THR A 8 HIS A 26 1 19 HELIX 2 2 SER A 29 ARG A 48 1 20 HELIX 3 3 ALA A 50 LEU A 69 1 20 HELIX 4 4 THR B 8 HIS B 26 1 19 HELIX 5 5 SER B 29 ARG B 48 1 20 HELIX 6 6 ALA B 50 SER B 68 1 19 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