HEADER TOXIN 28-MAY-20 6X6N TITLE NMR STRUCTURE OF THE PUTATIVE GTPASE-ACTIVATING (GAP) DOMAIN OF VOPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE VIRULENCE PROTEIN YOPE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: YOPE, ERS013201_01720; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 6 PPPARG4; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS GTPASE, GAP, TOXGAP, MITOCHONDRIA, MIRO, VIBRIO CHOLERAE, TOXIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR K.P.SMITH,W.LEE,M.TONELLI REVDAT 4 15-MAY-24 6X6N 1 REMARK REVDAT 3 14-JUN-23 6X6N 1 REMARK REVDAT 2 05-OCT-22 6X6N 1 JRNL REVDAT 1 22-DEC-21 6X6N 0 JRNL AUTH K.P.SMITH,W.LEE,M.TONELLI,Y.LEE,S.H.LIGHT,G.CORNILESCU, JRNL AUTH 2 S.CHAKRAVARTHY JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF THE JRNL TITL 2 MITOCHONDRIAL-TARGETED GTPASE-ACTIVATING PROTEIN (GAP) VOPE JRNL TITL 3 BY AN INTEGRATED NMR/SAXS APPROACH. JRNL REF PROTEIN SCI. V. 31 E4282 2022 JRNL REFN ESSN 1469-896X JRNL PMID 35137487 JRNL DOI 10.1002/PRO.4282 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PONDEROSA-C/S, PYMOL REMARK 3 AUTHORS : WOONGHEE LEE, JAIME L. STARK, JOHN L. MARKLEY REMARK 3 (PONDEROSA-C/S), SCHROEDINGER (PYMOL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6X6N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000245727. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.960 MM [U-13C; U-15N] VOPE GAP REMARK 210 DOMAIN, 10 MM HEPES PH 6.0, 150 REMARK 210 MM SODIUM CHLORIDE, 0.5 MM TCEP, REMARK 210 10 V/V D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D C(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D HCCH-COSY; 3D REMARK 210 HCCH-TOCSY; 2D 1H-13C HSQC; 2D REMARK 210 AROMATIC 1H-13C HSQC; 2D CBHD REMARK 210 AROMATIC; 2D CBHDHE AROMATIC; 3D REMARK 210 H(C)CH-TOCSY AROMATIC; 2D ARTSY; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN VNMRS; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 4.2, TOPSPIN 3.5, NMRFAM REMARK 210 -SPARKY, TALOS-N, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE NEUTRON SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : APS BEAMLINE 18D REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : APS REMARK 265 BEAMLINE INSTRUMENT : 18D REMARK 265 DETECTOR TYPE : PILATUS 3X 1M REMARK 265 DETECTOR MANUFACTURER DETAILS : DECTRIS REMARK 265 TEMPERATURE (KELVIN) : 298.15 REMARK 265 PH : 7.4 REMARK 265 NUMBER OF TIME FRAMES USED : 640 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 19.5 REMARK 265 SAMPLE BUFFER : 10 MM HEPES*HCL PH REMARK 265 7.4, 150 MM NACL, 0.5 REMARK 265 MM TCEP REMARK 265 DATA REDUCTION SOFTWARE : GNOM REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 20.23 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.09 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 7.8 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 265 SOFTWARE USED : NULL REMARK 265 SOFTWARE AUTHORS : NULL REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : NULL REMARK 265 CONFORMERS, NUMBER SUBMITTED : NULL REMARK 265 CONFORMERS, SELECTION CRITERIA : NULL REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 265 REMARK 265 OTHER DETAILS: NULL 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: 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 SER A 102 174.75 61.49 REMARK 500 1 GLU A 103 103.28 179.24 REMARK 500 1 GLU A 106 -147.76 -108.14 REMARK 500 1 ALA A 120 23.11 165.28 REMARK 500 1 SER A 123 -18.92 -179.26 REMARK 500 1 CYS A 155 15.64 85.46 REMARK 500 1 SER A 177 -159.15 -107.48 REMARK 500 2 ILE A 75 -34.54 -164.54 REMARK 500 2 SER A 102 -156.07 50.17 REMARK 500 2 GLU A 106 -167.55 -111.14 REMARK 500 2 ALA A 120 -112.11 171.13 REMARK 500 2 ASN A 121 72.44 -151.36 REMARK 500 2 SER A 123 -18.06 163.61 REMARK 500 2 ASP A 138 -75.23 -79.80 REMARK 500 2 ASP A 139 56.56 81.22 REMARK 500 3 GLU A 103 127.64 -170.70 REMARK 500 3 SER A 123 -18.50 -141.66 REMARK 500 3 CYS A 155 15.95 94.05 REMARK 500 4 GLU A 80 65.45 69.63 REMARK 500 4 ASP A 83 77.39 79.89 REMARK 500 4 GLU A 106 -162.85 -103.32 REMARK 500 4 LEU A 107 -9.06 -55.92 REMARK 500 4 SER A 123 -39.86 -159.79 REMARK 500 4 CYS A 155 -17.06 106.77 REMARK 500 4 GLU A 203 66.19 67.27 REMARK 500 5 ALA A 78 23.20 -161.88 REMARK 500 5 ASP A 83 -151.09 -167.92 REMARK 500 5 GLU A 103 120.88 -175.63 REMARK 500 5 GLU A 106 -88.12 -113.71 REMARK 500 5 ALA A 120 -119.21 170.05 REMARK 500 5 SER A 123 -17.03 165.00 REMARK 500 5 SER A 177 -168.15 -101.28 REMARK 500 5 GLU A 203 63.59 66.14 REMARK 500 6 TYR A 79 -176.76 76.49 REMARK 500 6 LYS A 82 -71.34 -117.23 REMARK 500 6 GLU A 106 -145.95 -110.69 REMARK 500 6 SER A 123 -17.53 -152.70 REMARK 500 6 ASP A 139 95.79 73.19 REMARK 500 6 CYS A 155 8.33 91.10 REMARK 500 6 PRO A 158 -178.57 -69.65 REMARK 500 7 ALA A 78 147.92 -170.15 REMARK 500 7 LYS A 82 -82.66 -151.74 REMARK 500 7 GLU A 106 -74.42 -104.12 REMARK 500 7 SER A 123 -25.72 -161.70 REMARK 500 7 ASP A 138 -77.68 -98.94 REMARK 500 7 ASP A 139 77.13 84.90 REMARK 500 7 CYS A 155 12.42 81.09 REMARK 500 7 GLU A 203 63.37 66.68 REMARK 500 8 ASP A 83 71.50 -169.48 REMARK 500 8 SER A 102 -163.87 53.58 REMARK 500 REMARK 500 THIS ENTRY HAS 145 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30756 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE PUTATIVE GTPASE-ACTIVATING (GAP) DOMAIN OF VOPE REMARK 900 RELATED ID: SASDJV3 RELATED DB: SASBDB REMARK 900 GTPASE-ACTIVATION PROTEIN (GAP) DOMAIN (73-204) OF VIBRIO CHOLERAE REMARK 900 OUTER PROTEIN E (VOPE) DBREF1 6X6N A 73 204 UNP A0A655XAV0_VIBCL DBREF2 6X6N A A0A655XAV0 73 204 SEQADV 6X6N GLY A 71 UNP A0A655XAV EXPRESSION TAG SEQADV 6X6N PRO A 72 UNP A0A655XAV EXPRESSION TAG SEQADV 6X6N ASP A 174 UNP A0A655XAV ALA 174 CONFLICT SEQRES 1 A 134 GLY PRO GLU ARG ILE SER LYS ALA TYR GLU SER LYS ASP SEQRES 2 A 134 VAL ARG LEU VAL ALA ARG ASP SER ALA PHE LEU GLY LEU SEQRES 3 A 134 GLN ARG ALA ILE ARG SER GLU ARG PHE GLU LEU ASP ASN SEQRES 4 A 134 PHE LYS SER ASN PHE PRO TYR LEU THR VAL ALA ASN GLY SEQRES 5 A 134 SER LEU ARG THR ILE VAL THR GLY LEU LYS GLY ILE VAL SEQRES 6 A 134 GLU PHE ASP ASP GLY GLN MET LYS ASP ILE ALA LYS GLU SEQRES 7 A 134 ILE LEU ASP THR GLN ILE CYS GLY VAL PRO PHE SER GLN SEQRES 8 A 134 PHE GLY THR CYS SER GLY SER ALA ARG ASP LEU VAL ASP SEQRES 9 A 134 ASN ALA SER TYR GLN GLN GLU LYS ILE ILE ILE LYS HIS SEQRES 10 A 134 LEU ASN GLU LEU PHE GLU LYS VAL ALA LEU HIS LEU VAL SEQRES 11 A 134 GLY ALA GLU VAL HELIX 1 AA1 ASP A 83 SER A 102 1 20 HELIX 2 AA2 ASN A 109 PHE A 114 1 6 HELIX 3 AA3 SER A 123 ASP A 139 1 17 HELIX 4 AA4 GLN A 141 ASP A 151 1 11 HELIX 5 AA5 SER A 160 GLY A 163 5 4 HELIX 6 AA6 SER A 166 ALA A 176 1 11 HELIX 7 AA7 SER A 177 VAL A 200 1 24 SHEET 1 AA1 2 GLN A 153 ILE A 154 0 SHEET 2 AA1 2 VAL A 157 PRO A 158 -1 O VAL A 157 N ILE A 154 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