HEADER TRANSFERASE 25-FEB-20 6M1C TITLE CRYSTAL STRUCTURE OF RSMD METHYLTRANSFERASE OF M. TUBERCULOSIS IN TITLE 2 COMPLEX WITH SINEFUNGIN REVEALS KEY INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: POSSIBLE METHYLTRANSFERASE (METHYLASE); 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 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: RV2966C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ROSSMANN FOLD, RSMD, RV2966C, M. TUBERCULOSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BIJPURIA,S.H.KHAN,A.KUMAR,B.TANEJA REVDAT 2 29-NOV-23 6M1C 1 REMARK REVDAT 1 02-JUN-21 6M1C 0 JRNL AUTH S.BIJPURIA,S.H.KHAN,A.KUMAR,B.TANEJA JRNL TITL CRYSTAL STRUCTURE OF RSMD METHYLTRANSFERASE OF M. JRNL TITL 2 TUBERCULOSIS IN COMPLEX WITH SINEFUNGIN REVEALS KEY JRNL TITL 3 INTERACTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7238 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.580 REMARK 3 FREE R VALUE TEST SET COUNT : 404 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 47.8000 - 3.4626 1.00 2377 121 0.1863 0.1899 REMARK 3 2 3.4626 - 2.7484 1.00 2253 137 0.2233 0.2933 REMARK 3 3 2.7484 - 2.4010 0.99 2204 146 0.2450 0.3264 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1434 REMARK 3 ANGLE : 0.838 1960 REMARK 3 CHIRALITY : 0.049 235 REMARK 3 PLANARITY : 0.006 253 REMARK 3 DIHEDRAL : 16.877 847 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 6M1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.887821 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3P9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MTRIS-HCL, 3.2 M POTASSIUM REMARK 280 ACETATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K 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 66.42733 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 33.21367 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 33.21367 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 66.42733 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: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 528 LIES ON A SPECIAL POSITION. 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 ARG A 19 REMARK 465 GLY A 20 REMARK 465 ALA A 186 REMARK 465 ASN A 187 REMARK 465 VAL A 188 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 0 OG REMARK 470 THR A 21 OG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 22 CB CG CD NE CZ NH1 NH2 REMARK 480 TYR A 122 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 GLU A 151 OE1 OE2 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 22 91.48 -160.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 402 DBREF 6M1C A 1 188 UNP I6XFS7 I6XFS7_MYCTU 1 188 SEQADV 6M1C SER A 0 UNP I6XFS7 EXPRESSION TAG SEQRES 1 A 189 SER MET THR ARG ILE ILE GLY GLY VAL ALA GLY GLY ARG SEQRES 2 A 189 ARG ILE ALA VAL PRO PRO ARG GLY THR ARG PRO THR THR SEQRES 3 A 189 ASP ARG VAL ARG GLU SER LEU PHE ASN ILE VAL THR ALA SEQRES 4 A 189 ARG ARG ASP LEU THR GLY LEU ALA VAL LEU ASP LEU TYR SEQRES 5 A 189 ALA GLY SER GLY ALA LEU GLY LEU GLU ALA LEU SER ARG SEQRES 6 A 189 GLY ALA ALA SER VAL LEU PHE VAL GLU SER ASP GLN ARG SEQRES 7 A 189 SER ALA ALA VAL ILE ALA ARG ASN ILE GLU ALA LEU GLY SEQRES 8 A 189 LEU SER GLY ALA THR LEU ARG ARG GLY ALA VAL ALA ALA SEQRES 9 A 189 VAL VAL ALA ALA GLY THR THR SER PRO VAL ASP LEU VAL SEQRES 10 A 189 LEU ALA ASP PRO PRO TYR ASN VAL ASP SER ALA ASP VAL SEQRES 11 A 189 ASP ALA ILE LEU ALA ALA LEU GLY THR ASN GLY TRP THR SEQRES 12 A 189 ARG GLU GLY THR VAL ALA VAL VAL GLU ARG ALA THR THR SEQRES 13 A 189 CYS ALA PRO LEU THR TRP PRO GLU GLY TRP ARG ARG TRP SEQRES 14 A 189 PRO GLN ARG VAL TYR GLY ASP THR ARG LEU GLU LEU ALA SEQRES 15 A 189 GLU ARG LEU PHE ALA ASN VAL HET SFG A 401 27 HET ACT A 402 4 HETNAM SFG SINEFUNGIN HETNAM ACT ACETATE ION HETSYN SFG ADENOSYL-ORNITHINE FORMUL 2 SFG C15 H23 N7 O5 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *53(H2 O) HELIX 1 AA1 THR A 25 ARG A 40 1 16 HELIX 2 AA2 GLY A 55 ARG A 64 1 10 HELIX 3 AA3 ASP A 75 GLY A 90 1 16 HELIX 4 AA4 ALA A 100 ALA A 107 1 8 HELIX 5 AA5 ASP A 125 ASN A 139 1 15 SHEET 1 AA1 7 ALA A 94 ARG A 98 0 SHEET 2 AA1 7 SER A 68 GLU A 73 1 N PHE A 71 O THR A 95 SHEET 3 AA1 7 ALA A 46 LEU A 50 1 N ASP A 49 O LEU A 70 SHEET 4 AA1 7 LEU A 115 ALA A 118 1 O LEU A 117 N LEU A 50 SHEET 5 AA1 7 VAL A 147 ALA A 153 1 O VAL A 147 N VAL A 116 SHEET 6 AA1 7 THR A 176 ARG A 183 -1 O ARG A 177 N ARG A 152 SHEET 7 AA1 7 TRP A 165 ARG A 167 -1 N ARG A 166 O GLU A 182 SHEET 1 AA2 7 ALA A 94 ARG A 98 0 SHEET 2 AA2 7 SER A 68 GLU A 73 1 N PHE A 71 O THR A 95 SHEET 3 AA2 7 ALA A 46 LEU A 50 1 N ASP A 49 O LEU A 70 SHEET 4 AA2 7 LEU A 115 ALA A 118 1 O LEU A 117 N LEU A 50 SHEET 5 AA2 7 VAL A 147 ALA A 153 1 O VAL A 147 N VAL A 116 SHEET 6 AA2 7 THR A 176 ARG A 183 -1 O ARG A 177 N ARG A 152 SHEET 7 AA2 7 ARG A 171 TYR A 173 -1 N TYR A 173 O THR A 176 SITE 1 AC1 18 ARG A 22 PRO A 23 THR A 24 TYR A 51 SITE 2 AC1 18 ALA A 52 GLY A 53 SER A 54 GLU A 73 SITE 3 AC1 18 SER A 74 ASP A 75 SER A 78 VAL A 101 SITE 4 AC1 18 ASP A 119 PRO A 121 ACT A 402 HOH A 502 SITE 5 AC1 18 HOH A 530 HOH A 536 SITE 1 AC2 7 ARG A 22 PRO A 23 THR A 24 ASP A 119 SITE 2 AC2 7 GLU A 151 SFG A 401 HOH A 511 CRYST1 55.191 55.191 99.641 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 0.018119 0.010461 0.000000 0.00000 SCALE2 0.000000 0.020922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010036 0.00000