HEADER TOXIN 25-FEB-20 6Y5U TITLE MENT3 (AKA TGLT), NUCLEOTIDYLTRANSFERASE TOXIN RV1045 FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RV1045; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 GENE: RV1045; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDYLTRANSFERASE TOXIN-ANTITOXIN SYSTEM MYCOBACTERIUM KEYWDS 2 TUBERCULOSIS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR T.R.BLOWER,B.USHER REVDAT 4 20-JAN-21 6Y5U 1 TITLE REVDAT 3 30-SEP-20 6Y5U 1 JRNL REVDAT 2 23-SEP-20 6Y5U 1 JRNL REVDAT 1 16-SEP-20 6Y5U 0 JRNL AUTH Y.CAI,B.USHER,C.GUTIERREZ,A.TOLCAN,M.MANSOUR,P.C.FINERAN, JRNL AUTH 2 C.CONDON,O.NEYROLLES,P.GENEVAUX,T.R.BLOWER JRNL TITL A NUCLEOTIDYLTRANSFERASE TOXIN INHIBITS GROWTH OF JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS THROUGH INACTIVATION OF TRNA JRNL TITL 3 ACCEPTOR STEMS. JRNL REF SCI ADV V. 6 B6651 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 32923609 JRNL DOI 10.1126/SCIADV.ABB6651 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 49001 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 52.9700 - 4.0900 1.00 2863 178 0.1773 0.1827 REMARK 3 2 4.0900 - 3.2400 1.00 2794 156 0.1779 0.2011 REMARK 3 3 3.2400 - 2.8300 1.00 2731 185 0.2043 0.2227 REMARK 3 4 2.8300 - 2.5800 1.00 2759 124 0.2177 0.2605 REMARK 3 5 2.5800 - 2.3900 1.00 2750 135 0.2156 0.2645 REMARK 3 6 2.3900 - 2.2500 1.00 2779 114 0.2175 0.2796 REMARK 3 7 2.2500 - 2.1400 1.00 2741 134 0.2169 0.2599 REMARK 3 8 2.1400 - 2.0400 1.00 2741 132 0.2044 0.2543 REMARK 3 9 2.0400 - 1.9700 1.00 2761 106 0.2135 0.2288 REMARK 3 10 1.9700 - 1.9000 1.00 2742 117 0.2210 0.2566 REMARK 3 11 1.9000 - 1.8400 1.00 2689 178 0.2172 0.2312 REMARK 3 12 1.8400 - 1.7900 1.00 2710 141 0.2215 0.2504 REMARK 3 13 1.7900 - 1.7400 1.00 2738 109 0.2358 0.2876 REMARK 3 14 1.7400 - 1.7000 1.00 2737 143 0.2437 0.2997 REMARK 3 15 1.7000 - 1.6600 1.00 2653 173 0.2637 0.2687 REMARK 3 16 1.6600 - 1.6200 1.00 2725 160 0.2690 0.3026 REMARK 3 17 1.6200 - 1.5900 0.99 2651 152 0.3074 0.3136 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.207 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.706 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2260 REMARK 3 ANGLE : 0.937 3086 REMARK 3 CHIRALITY : 0.053 361 REMARK 3 PLANARITY : 0.007 404 REMARK 3 DIHEDRAL : 22.160 830 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 52.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE HYDRATE 0.1 M REMARK 280 TRIS PH 8.5 25% W/V PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.01733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.00867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.00867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.01733 REMARK 290 REMARK 290 REMARK: 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 292 REMARK 465 ARG A 293 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 ARG A 87 -39.11 -151.46 REMARK 500 ILE A 89 -93.72 -118.59 REMARK 500 ALA A 152 -127.60 48.83 REMARK 500 GLU A 199 -56.64 -22.64 REMARK 500 ARG A 205 41.53 -83.29 REMARK 500 LEU A 220 -129.45 55.23 REMARK 500 GLN A 240 -112.81 -112.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Y5U A 2 293 UNP P96356 P96356_MYCTU 2 293 SEQRES 1 A 292 THR LYS PRO TYR SER SER PRO PRO THR ASN LEU ARG SER SEQRES 2 A 292 LEU ARG ASP ARG LEU THR GLN VAL ALA GLU ARG GLN GLY SEQRES 3 A 292 VAL VAL PHE GLY ARG LEU GLN ARG HIS VAL ALA MET ILE SEQRES 4 A 292 VAL VAL ALA GLN PHE ALA ALA THR LEU THR ASP ASP THR SEQRES 5 A 292 GLY ALA PRO LEU LEU LEU VAL LYS GLY GLY SER SER LEU SEQRES 6 A 292 GLU LEU ARG ARG GLY ILE PRO ASP SER ARG THR SEP LYS SEQRES 7 A 292 ASP PHE ASP THR VAL ALA ARG ARG ASP ILE GLU LEU ILE SEQRES 8 A 292 HIS GLU GLN LEU ALA ASP ALA GLY GLU THR GLY TRP GLU SEQRES 9 A 292 GLY PHE THR ALA ILE PHE THR ALA PRO GLU GLU ILE ASP SEQRES 10 A 292 VAL PRO GLY MET PRO VAL LYS PRO ARG ARG PHE THR ALA SEQRES 11 A 292 LYS LEU SER TYR ARG GLY ARG ALA PHE ALA THR VAL PRO SEQRES 12 A 292 ILE GLU VAL SER SER VAL GLU ALA GLY ASN ALA ASP GLN SEQRES 13 A 292 PHE ASP THR LEU THR SER ASP ALA LEU GLY LEU VAL GLY SEQRES 14 A 292 VAL PRO ALA ALA VAL ALA VAL PRO CYS MET THR ILE PRO SEQRES 15 A 292 TRP GLN ILE ALA GLN LYS LEU HIS ALA VAL THR ALA VAL SEQRES 16 A 292 LEU GLU GLU PRO LYS VAL ASN ASP ARG ALA HIS ASP LEU SEQRES 17 A 292 VAL ASP LEU GLN LEU LEU GLU GLY LEU LEU LEU ASP ALA SEQRES 18 A 292 ASP LEU MET PRO THR ARG SER ALA CYS ILE ALA ILE PHE SEQRES 19 A 292 GLU ALA ARG ALA GLN HIS PRO TRP PRO PRO ARG VAL ALA SEQRES 20 A 292 THR LEU PRO HIS TRP PRO LEU ILE TYR ALA GLY ALA LEU SEQRES 21 A 292 GLU GLY LEU ASP HIS LEU GLU LEU ALA ARG THR VAL ASP SEQRES 22 A 292 ALA ALA ALA GLN ALA VAL GLN ARG PHE VAL ALA ARG ILE SEQRES 23 A 292 ASP ARG ALA THR LYS ARG MODRES 6Y5U SEP A 78 SER MODIFIED RESIDUE HET SEP A 78 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 HOH *281(H2 O) HELIX 1 AA1 ASN A 11 GLY A 27 1 17 HELIX 2 AA2 VAL A 29 THR A 48 1 20 HELIX 3 AA3 GLY A 62 GLY A 71 1 10 HELIX 4 AA4 ILE A 72 SER A 75 5 4 HELIX 5 AA5 GLU A 90 GLY A 103 1 14 HELIX 6 AA6 LEU A 166 GLY A 170 5 5 HELIX 7 AA7 THR A 181 THR A 194 1 14 HELIX 8 AA8 ALA A 206 LEU A 220 1 15 HELIX 9 AA9 LEU A 224 ALA A 239 1 16 HELIX 10 AB1 HIS A 252 LEU A 261 1 10 HELIX 11 AB2 THR A 272 ALA A 290 1 19 SHEET 1 AA1 5 LEU A 58 LYS A 61 0 SHEET 2 AA1 5 PHE A 81 ALA A 85 -1 O ASP A 82 N LYS A 61 SHEET 3 AA1 5 ARG A 138 SER A 149 1 O SER A 148 N ALA A 85 SHEET 4 AA1 5 ARG A 127 TYR A 135 -1 N LEU A 133 O PHE A 140 SHEET 5 AA1 5 PHE A 107 PHE A 111 -1 N ILE A 110 O LYS A 132 SHEET 1 AA2 5 LEU A 58 LYS A 61 0 SHEET 2 AA2 5 PHE A 81 ALA A 85 -1 O ASP A 82 N LYS A 61 SHEET 3 AA2 5 ARG A 138 SER A 149 1 O SER A 148 N ALA A 85 SHEET 4 AA2 5 ARG A 127 TYR A 135 -1 N LEU A 133 O PHE A 140 SHEET 5 AA2 5 GLU A 115 GLU A 116 -1 N GLU A 115 O ARG A 128 SHEET 1 AA3 2 ASP A 159 LEU A 161 0 SHEET 2 AA3 2 VAL A 177 CYS A 179 -1 O CYS A 179 N ASP A 159 LINK C THR A 77 N SEP A 78 1555 1555 1.33 LINK C SEP A 78 N LYS A 79 1555 1555 1.33 CISPEP 1 TRP A 243 PRO A 244 0 -3.89 CRYST1 95.410 95.410 69.026 90.00 90.00 120.00 P 32 2 1 6 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 0.010481 0.006051 0.000000 0.00000 SCALE2 0.000000 0.012103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014487 0.00000