HEADER TOXIN 24-MAR-22 7ZBQ TITLE STRUCTURE OF THE ADP-RIBOSYLTRANSFERASE TCCC3HVR FROM PHOTORHABDUS TITLE 2 LUMINESCENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TCCC3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTORHABDUS LUMINESCENS; SOURCE 3 ORGANISM_TAXID: 29488; SOURCE 4 GENE: TCCC3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL KEYWDS ADP-RIBOSYLATION, R-S-E MOTIF, ACTIN MODIFICATION, TOXIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.LINDEMANN,A.BELYY,D.FRIEDRICH,P.SCHMIEDER,B.BARDIAUX,D.RODERER, AUTHOR 2 J.FUNK,J.PROTZE,P.BIELING,H.OSCHKINAT,S.RAUNSER REVDAT 2 03-AUG-22 7ZBQ 1 JRNL REVDAT 1 29-JUN-22 7ZBQ 0 JRNL AUTH A.BELYY,F.LINDEMANN,D.RODERER,J.FUNK,B.BARDIAUX,J.PROTZE, JRNL AUTH 2 P.BIELING,H.OSCHKINAT,S.RAUNSER JRNL TITL MECHANISM OF THREONINE ADP-RIBOSYLATION OF F-ACTIN BY A TC JRNL TITL 2 TOXIN. JRNL REF NAT COMMUN V. 13 4202 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35858890 JRNL DOI 10.1038/S41467-022-31836-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STANDARD ARIA/CNS WATER REFINEMENT REMARK 3 PROTOCOL REMARK 4 REMARK 4 7ZBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292121774. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280 REMARK 210 PH : 7.8 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM NON-EXCHANGEABLE-D, U REMARK 210 -13C, U-15N TCART, 20 MM HEPES, REMARK 210 150 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 500 UM [U-13C; U-15N] REMARK 210 TCART, 20 MM D11-TRIS, 150 MM REMARK 210 SODIUM CHLORIDE, 100% D2O; 500 REMARK 210 UM [U-13C; U-15N] TCART, 20 MM REMARK 210 HEPES, 150 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HCCH-TOCSY; 3D HNCA; 2D 1H-1H REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5PL6, CCPNMR ANALYSIS REMARK 210 2.4.2, ARIA 2.3.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 97 REMARK 465 SER A 98 REMARK 465 THR A 99 REMARK 465 THR A 100 REMARK 465 SER A 101 REMARK 465 ARG A 282 REMARK 465 GLY A 283 REMARK 465 THR A 284 REMARK 465 LEU A 285 REMARK 465 GLU A 286 REMARK 465 VAL A 287 REMARK 465 LEU A 288 REMARK 465 PHE A 289 REMARK 465 GLN A 290 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 TYR A 180 CE1 TYR A 180 CZ -0.084 REMARK 500 1 TYR A 180 CZ TYR A 180 CE2 0.080 REMARK 500 5 TYR A 180 CE1 TYR A 180 CZ -0.084 REMARK 500 5 TYR A 180 CZ TYR A 180 CE2 0.080 REMARK 500 7 TYR A 180 CE1 TYR A 180 CZ -0.087 REMARK 500 7 TYR A 180 CZ TYR A 180 CE2 0.085 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 ASP A 153 36.27 -92.02 REMARK 500 1 THR A 154 46.48 -78.35 REMARK 500 1 ASN A 156 -16.19 77.31 REMARK 500 1 VAL A 190 -27.11 82.09 REMARK 500 1 ASN A 236 -92.00 43.37 REMARK 500 1 PRO A 246 -19.52 -49.17 REMARK 500 1 PRO A 260 -161.69 -72.99 REMARK 500 2 THR A 154 37.86 -85.84 REMARK 500 2 ASN A 156 -16.52 75.86 REMARK 500 2 SER A 188 40.74 -85.80 REMARK 500 2 VAL A 190 -17.27 90.63 REMARK 500 2 SER A 204 -81.10 -89.73 REMARK 500 2 THR A 234 138.66 176.79 REMARK 500 2 ASN A 236 -83.57 65.62 REMARK 500 2 PRO A 246 3.10 -61.89 REMARK 500 2 GLU A 249 0.51 -66.41 REMARK 500 3 THR A 154 48.66 -82.59 REMARK 500 3 ASN A 156 44.92 73.99 REMARK 500 3 VAL A 190 -28.58 82.95 REMARK 500 3 SER A 204 105.86 -59.62 REMARK 500 3 SER A 205 -71.35 67.39 REMARK 500 3 LEU A 229 78.82 -114.29 REMARK 500 3 PRO A 246 -3.23 -58.76 REMARK 500 3 PRO A 260 -176.97 -68.61 REMARK 500 4 THR A 154 45.83 -89.56 REMARK 500 4 ASN A 156 -16.93 74.67 REMARK 500 4 VAL A 190 -26.73 88.20 REMARK 500 4 SER A 204 -85.61 65.48 REMARK 500 4 ARG A 233 -58.30 -124.17 REMARK 500 5 LYS A 187 40.91 -87.99 REMARK 500 5 SER A 188 22.20 -148.09 REMARK 500 5 VAL A 190 -16.07 112.06 REMARK 500 5 LEU A 229 76.28 -119.23 REMARK 500 5 THR A 234 136.71 -173.25 REMARK 500 5 ASN A 236 -83.29 62.69 REMARK 500 6 LYS A 152 48.89 -84.50 REMARK 500 6 VAL A 190 -26.92 88.65 REMARK 500 6 SER A 205 -57.18 -145.95 REMARK 500 6 ARG A 233 -47.65 -130.99 REMARK 500 6 THR A 234 136.64 171.27 REMARK 500 7 VAL A 190 -38.64 82.24 REMARK 500 7 ILE A 272 106.64 -54.18 REMARK 500 8 THR A 154 30.47 -99.33 REMARK 500 8 VAL A 190 -25.03 90.98 REMARK 500 8 ASN A 236 -95.12 61.89 REMARK 500 8 PRO A 260 -157.00 -70.99 REMARK 500 8 ASP A 263 37.48 -95.25 REMARK 500 8 ILE A 272 109.26 -59.30 REMARK 500 9 VAL A 190 -21.50 89.91 REMARK 500 9 SER A 205 -70.81 70.90 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34717 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE ADP-RIBOSYLTRANSFERASE TCCC3HVR FROM PHOTORHABDUS REMARK 900 LUMINESCENS DBREF 7ZBQ A 98 282 UNP Q8GF97 Q8GF97_PHOLU 776 960 SEQADV 7ZBQ MET A 97 UNP Q8GF97 INITIATING METHIONINE SEQADV 7ZBQ GLY A 283 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ THR A 284 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ LEU A 285 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ GLU A 286 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ VAL A 287 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ LEU A 288 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ PHE A 289 UNP Q8GF97 EXPRESSION TAG SEQADV 7ZBQ GLN A 290 UNP Q8GF97 EXPRESSION TAG SEQRES 1 A 194 MET SER THR THR SER THR ASN LEU GLN LYS LYS SER PHE SEQRES 2 A 194 THR LEU TYR ARG ALA ASP ASN ARG SER PHE GLU GLU MET SEQRES 3 A 194 GLN SER LYS PHE PRO GLU GLY PHE LYS ALA TRP THR PRO SEQRES 4 A 194 LEU ASP THR LYS MET ALA ARG GLN PHE ALA SER ILE PHE SEQRES 5 A 194 ILE GLY GLN LYS ASP THR SER ASN LEU PRO LYS GLU THR SEQRES 6 A 194 VAL LYS ASN ILE SER THR TRP GLY ALA LYS PRO LYS LEU SEQRES 7 A 194 LYS ASP LEU SER ASN TYR ILE LYS TYR THR LYS ASP LYS SEQRES 8 A 194 SER THR VAL TRP VAL SER THR ALA ILE ASN THR GLU ALA SEQRES 9 A 194 GLY GLY GLN SER SER GLY ALA PRO LEU HIS LYS ILE ASP SEQRES 10 A 194 MET ASP LEU TYR GLU PHE ALA ILE ASP GLY GLN LYS LEU SEQRES 11 A 194 ASN PRO LEU PRO GLU GLY ARG THR LYS ASN MET VAL PRO SEQRES 12 A 194 SER LEU LEU LEU ASP THR PRO GLN ILE GLU THR SER SER SEQRES 13 A 194 ILE ILE ALA LEU ASN HIS GLY PRO VAL ASN ASP ALA GLU SEQRES 14 A 194 ILE SER PHE LEU THR THR ILE PRO LEU LYS ASN VAL LYS SEQRES 15 A 194 PRO HIS LYS ARG GLY THR LEU GLU VAL LEU PHE GLN HELIX 1 AA1 SER A 118 LYS A 125 1 8 HELIX 2 AA2 ASP A 137 SER A 146 1 10 HELIX 3 AA3 ILE A 147 GLY A 150 5 4 HELIX 4 AA4 PRO A 158 TRP A 168 1 11 HELIX 5 AA5 LYS A 173 THR A 184 1 12 HELIX 6 AA6 GLN A 247 SER A 251 5 5 SHEET 1 AA1 9 LEU A 226 PRO A 228 0 SHEET 2 AA1 9 VAL A 277 LYS A 278 0 SHEET 3 AA1 9 LYS A 106 ALA A 114 0 SHEET 4 AA1 9 VAL A 192 ALA A 195 -1 O ALA A 195 N TYR A 112 SHEET 5 AA1 9 GLU A 265 PHE A 268 -1 O PHE A 268 N VAL A 192 SHEET 6 AA1 9 ILE A 254 HIS A 258 -1 N LEU A 256 O SER A 267 SHEET 7 AA1 9 SER A 240 LEU A 243 -1 N LEU A 242 O ALA A 255 SHEET 8 AA1 9 LEU A 209 ILE A 221 -1 N TYR A 217 O LEU A 243 SHEET 9 AA1 9 VAL A 277 LYS A 278 -1 O LYS A 278 N LYS A 211 SHEET 1 AA2 2 GLY A 129 PHE A 130 0 SHEET 2 AA2 2 ILE A 272 PRO A 273 -1 O ILE A 272 N PHE A 130 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