HEADER TOXIN 24-FEB-20 6Y56 TITLE MENT4, NUCLEOTIDYLTRANSFERASE TOXIN RV2826C FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS H37RV COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 GENE: RV2826C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDYLTRANSFERASE TOXIN-ANTITOXIN SYSTEM TUBERCULOSIS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR B.USHER,T.R.BLOWER REVDAT 5 15-MAY-24 6Y56 1 REMARK REVDAT 4 20-JAN-21 6Y56 1 TITLE REVDAT 3 30-SEP-20 6Y56 1 JRNL REVDAT 2 23-SEP-20 6Y56 1 JRNL REVDAT 1 16-SEP-20 6Y56 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. 1.23 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 75481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 3598 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 54.6900 - 3.6400 1.00 2891 140 0.1619 0.1576 REMARK 3 2 3.6400 - 2.8900 1.00 2855 123 0.1687 0.1692 REMARK 3 3 2.8900 - 2.5300 1.00 2830 131 0.1765 0.1647 REMARK 3 4 2.5300 - 2.3000 1.00 2781 167 0.1718 0.1986 REMARK 3 5 2.3000 - 2.1300 1.00 2785 150 0.1667 0.1872 REMARK 3 6 2.1300 - 2.0100 1.00 2837 120 0.1698 0.1831 REMARK 3 7 2.0100 - 1.9000 1.00 2788 145 0.1729 0.1848 REMARK 3 8 1.9000 - 1.8200 1.00 2779 160 0.1820 0.1964 REMARK 3 9 1.8200 - 1.7500 1.00 2779 142 0.1888 0.2087 REMARK 3 10 1.7500 - 1.6900 1.00 2814 122 0.1796 0.2220 REMARK 3 11 1.6900 - 1.6400 1.00 2832 126 0.1922 0.1941 REMARK 3 12 1.6400 - 1.5900 1.00 2778 149 0.1847 0.2072 REMARK 3 13 1.5900 - 1.5500 1.00 2812 138 0.1857 0.2102 REMARK 3 14 1.5500 - 1.5100 1.00 2789 125 0.1958 0.2196 REMARK 3 15 1.5100 - 1.4800 1.00 2825 100 0.2009 0.2311 REMARK 3 16 1.4800 - 1.4500 1.00 2794 136 0.2106 0.2427 REMARK 3 17 1.4500 - 1.4200 1.00 2782 139 0.2289 0.2673 REMARK 3 18 1.4200 - 1.3900 1.00 2788 153 0.2450 0.2550 REMARK 3 19 1.3900 - 1.3700 1.00 2755 149 0.2524 0.2453 REMARK 3 20 1.3700 - 1.3400 1.00 2796 165 0.2603 0.2717 REMARK 3 21 1.3400 - 1.3200 0.99 2720 147 0.2696 0.2791 REMARK 3 22 1.3200 - 1.3000 0.99 2782 136 0.2731 0.2926 REMARK 3 23 1.3000 - 1.2800 0.99 2714 139 0.2846 0.2855 REMARK 3 24 1.2800 - 1.2600 0.97 2758 140 0.3008 0.3230 REMARK 3 25 1.2600 - 1.2500 0.91 2557 122 0.3166 0.3508 REMARK 3 26 1.2500 - 1.2300 0.83 2262 134 0.3291 0.3259 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.641 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.58 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 : 0.005 2368 REMARK 3 ANGLE : 0.829 3209 REMARK 3 CHIRALITY : 0.071 356 REMARK 3 PLANARITY : 0.005 424 REMARK 3 DIHEDRAL : 19.235 878 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 6Y56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-19 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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9781 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 : 75996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 54.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 1.970 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 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 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.90200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 ALA A 2 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 46 -62.90 -133.18 REMARK 500 ARG A 122 40.30 -92.20 REMARK 500 ASP A 266 48.25 -84.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Y56 A 2 294 UNP P71626 P71626_MYCTU 2 294 SEQRES 1 A 293 ALA GLY LEU THR ARG ALA LEU VAL ALA ARG HIS ALA LEU SEQRES 2 A 293 GLY ARG ALA GLU ALA TYR ASP ALA ALA LEU LEU ASP VAL SEQRES 3 A 293 ALA GLN ASP HIS LEU LEU TYR LEU LEU SER GLN THR VAL SEQRES 4 A 293 GLN PHE GLY ASP ASN ARG LEU VAL PHE LYS GLY GLY THR SEQRES 5 A 293 SER LEU ARG LYS CYS ARG LEU GLY ASN VAL GLY ARG PHE SEQRES 6 A 293 SER THR ASP LEU ASP PHE SER ALA PRO ASP ASP GLU VAL SEQRES 7 A 293 VAL LEU GLU VAL CYS GLU LEU ILE ASP GLY ALA ARG VAL SEQRES 8 A 293 GLY GLY PHE GLU PHE GLY VAL GLN SER THR ARG GLY ASP SEQRES 9 A 293 GLY ARG HIS TRP GLN LEU ARG VAL ARG HIS THR GLU LEU SEQRES 10 A 293 GLY GLU PRO ARG ILE VAL ALA SER VAL GLU PHE ALA ARG SEQRES 11 A 293 ARG PRO LEU ALA LEU PRO SER GLU LEU LEU ALA PHE ILE SEQRES 12 A 293 GLN LEU PRO ILE HIS LYS ALA TYR GLY PHE GLY LEU PRO SEQRES 13 A 293 THR LEU PRO VAL VAL ALA GLU ALA GLU ALA CYS ALA GLU SEQRES 14 A 293 LYS LEU ALA ARG TYR ARG ARG VAL ALA LEU ALA ARG ASP SEQRES 15 A 293 LEU TYR ASP LEU ASN HIS PHE ALA SER ARG THR ILE ASP SEQRES 16 A 293 GLU PRO LEU VAL ARG ARG LEU TRP VAL LEU LYS VAL TRP SEQRES 17 A 293 GLY ASP VAL VAL ASP ASP ARG ARG GLY THR ARG PRO LEU SEQRES 18 A 293 ARG VAL GLU ASP VAL LEU ALA ALA ARG SER GLU HIS ASP SEQRES 19 A 293 PHE GLN PRO ASP SER ILE GLY VAL LEU THR ARG PRO VAL SEQRES 20 A 293 ALA MET ALA ALA TRP GLU ALA ARG VAL ARG LYS ARG PHE SEQRES 21 A 293 ALA PHE LEU THR ASP LEU ASP ALA ASP GLU GLN ARG TRP SEQRES 22 A 293 ALA ALA CYS ASP GLU ARG HIS ARG ARG GLU VAL GLU ASN SEQRES 23 A 293 ALA LEU ALA VAL LEU ARG SER FORMUL 2 HOH *327(H2 O) HELIX 1 AA1 THR A 5 ALA A 13 1 9 HELIX 2 AA2 ARG A 16 GLU A 18 5 3 HELIX 3 AA3 ALA A 19 VAL A 40 1 22 HELIX 4 AA4 GLY A 51 ARG A 59 1 9 HELIX 5 AA5 LEU A 60 GLY A 64 5 5 HELIX 6 AA6 ASP A 76 ASP A 88 1 13 HELIX 7 AA7 LEU A 146 TYR A 152 5 7 HELIX 8 AA8 ALA A 163 ARG A 176 1 14 HELIX 9 AA9 LEU A 180 ALA A 191 1 12 HELIX 10 AB1 ASP A 196 ASP A 214 1 19 HELIX 11 AB2 VAL A 224 ALA A 229 1 6 HELIX 12 AB3 SER A 232 PHE A 236 5 5 HELIX 13 AB4 SER A 240 THR A 245 1 6 HELIX 14 AB5 ALA A 249 PHE A 261 1 13 HELIX 15 AB6 ALA A 262 ASP A 266 5 5 HELIX 16 AB7 ASP A 268 ALA A 275 1 8 HELIX 17 AB8 ALA A 276 CYS A 277 5 2 HELIX 18 AB9 ASP A 278 ARG A 280 5 3 HELIX 19 AC1 HIS A 281 SER A 294 1 14 SHEET 1 AA1 6 VAL A 48 LYS A 50 0 SHEET 2 AA1 6 ASP A 69 SER A 73 -1 O SER A 73 N VAL A 48 SHEET 3 AA1 6 SER A 126 ALA A 130 1 O ALA A 130 N PHE A 72 SHEET 4 AA1 6 HIS A 108 HIS A 115 -1 N TRP A 109 O VAL A 127 SHEET 5 AA1 6 PHE A 95 SER A 101 -1 N GLN A 100 O GLN A 110 SHEET 6 AA1 6 ARG A 91 VAL A 92 -1 N VAL A 92 O PHE A 95 SHEET 1 AA2 2 GLU A 139 ALA A 142 0 SHEET 2 AA2 2 THR A 158 VAL A 161 -1 O VAL A 161 N GLU A 139 CISPEP 1 ARG A 220 PRO A 221 0 -1.11 CISPEP 2 ARG A 246 PRO A 247 0 -0.68 CRYST1 42.268 57.804 54.734 90.00 92.29 90.00 P 1 21 1 2 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 0.023659 0.000000 0.000947 0.00000 SCALE2 0.000000 0.017300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018285 0.00000