HEADER TRANSFERASE 24-JAN-23 8FX9 TITLE CRYSTAL STRUCUTRE OF MYCOBACTERIUM TUBERCULOSIS MYCOTHIOL-S- TITLE 2 TRANSFERASE ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOTHIOL-S-TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: RV0443; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MYCOTHIOL, DINB SUPERFAMILY, TRANSFERASE, APO, METALLOENZYME EXPDTA X-RAY DIFFRACTION AUTHOR J.J.LINDENBERGER,Y.P.JAYASINGHE,D.R.RONNING REVDAT 1 05-APR-23 8FX9 0 JRNL AUTH Y.P.JAYASINGHE,M.T.BANCO,J.J.LINDENBERGER,L.FAVROT, JRNL AUTH 2 Z.PALCEKOVA,M.JACKSON,S.MANABE,D.R.RONNING JRNL TITL THE MYCOBACTERIUM TUBERCULOSIS MYCOTHIOL S -TRANSFERASE IS JRNL TITL 2 DIVALENT METAL-DEPENDENT FOR MYCOTHIOL BINDING AND TRANSFER. JRNL REF RSC MED CHEM V. 14 491 2023 JRNL REFN ESSN 2632-8682 JRNL PMID 36970142 JRNL DOI 10.1039/D2MD00401A REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 31474 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.330 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 29.4300 - 3.2800 0.80 2005 136 0.1693 0.1866 REMARK 3 2 3.2800 - 2.6000 1.00 2392 162 0.1837 0.2269 REMARK 3 3 2.6000 - 2.2900 0.99 2155 144 0.1849 0.2072 REMARK 3 4 2.2100 - 2.0600 0.98 1677 113 0.1806 0.2006 REMARK 3 5 2.0600 - 1.9200 0.81 1901 130 0.2117 0.2414 REMARK 3 6 1.9200 - 1.8000 0.76 1780 120 0.2245 0.2740 REMARK 3 7 1.8000 - 1.7100 1.00 2337 158 0.1808 0.2161 REMARK 3 8 1.7100 - 1.6400 1.00 2343 160 0.1761 0.2077 REMARK 3 9 1.6400 - 1.5800 1.00 2317 155 0.1745 0.1754 REMARK 3 10 1.5800 - 1.5200 1.00 2299 156 0.1814 0.2235 REMARK 3 11 1.5200 - 1.4700 0.99 2326 158 0.1998 0.2413 REMARK 3 12 1.4700 - 1.4300 0.96 2229 150 0.2181 0.2371 REMARK 3 13 1.4300 - 1.3900 0.87 2019 136 0.2290 0.2720 REMARK 3 14 1.3900 - 1.3600 0.73 1701 115 0.2401 0.2918 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.450 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 : 0.006 1405 REMARK 3 ANGLE : 0.770 1928 REMARK 3 CHIRALITY : 0.064 216 REMARK 3 PLANARITY : 0.008 254 REMARK 3 DIHEDRAL : 3.840 199 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 8FX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-14 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.98500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.98500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.68850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.44550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.68850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.44550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.98500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.68850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.44550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 24.98500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.68850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.44550 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 65.37700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -24.98500 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 THR A 137 OG1 CG2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 513 DISTANCE = 6.00 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8F5V RELATED DB: PDB DBREF 8FX9 A 2 170 UNP O53728 O53728_MYCTU 2 170 SEQADV 8FX9 PRO A 1 UNP O53728 EXPRESSION TAG SEQRES 1 A 170 PRO ALA SER THR ASP ALA ALA ALA GLN GLU LEU LEU ARG SEQRES 2 A 170 ASP ALA PHE THR ARG LEU ILE GLU HIS VAL ASP GLU LEU SEQRES 3 A 170 THR ASP GLY LEU THR ASP GLN LEU ALA CYS TYR ARG PRO SEQRES 4 A 170 THR PRO SER ALA ASN SER ILE ALA TRP LEU LEU TRP HIS SEQRES 5 A 170 SER ALA ARG VAL GLN ASP ILE GLN VAL ALA HIS VAL ALA SEQRES 6 A 170 GLY VAL GLU GLU VAL TRP THR ARG ASP GLY TRP VAL ASP SEQRES 7 A 170 ARG PHE GLY LEU ASP LEU PRO ARG HIS ASP THR GLY TYR SEQRES 8 A 170 GLY HIS ARG PRO GLU ASP VAL ALA LYS VAL ARG ALA PRO SEQRES 9 A 170 ALA ASP LEU LEU SER GLY TYR TYR HIS ALA VAL HIS LYS SEQRES 10 A 170 LEU THR LEU GLU TYR ILE ALA GLY MET THR ALA ASP GLU SEQRES 11 A 170 LEU SER ARG VAL VAL ASP THR SER TRP ASN PRO PRO VAL SEQRES 12 A 170 THR VAL SER ALA ARG LEU VAL SER ILE VAL ASP ASP CYS SEQRES 13 A 170 ALA GLN HIS LEU GLY GLN ALA ALA TYR LEU ARG GLY ILE SEQRES 14 A 170 ALA HET CL A 201 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *213(H2 O) HELIX 1 AA1 ALA A 2 THR A 4 5 3 HELIX 2 AA2 ASP A 5 ASP A 28 1 24 HELIX 3 AA3 THR A 31 TYR A 37 1 7 HELIX 4 AA4 SER A 45 GLY A 66 1 22 HELIX 5 AA5 GLU A 69 ASP A 74 1 6 HELIX 6 AA6 GLY A 75 GLY A 81 1 7 HELIX 7 AA7 ARG A 94 VAL A 101 5 8 HELIX 8 AA8 PRO A 104 ALA A 124 1 21 HELIX 9 AA9 THR A 127 ARG A 133 1 7 HELIX 10 AB1 VAL A 145 ALA A 170 1 26 SHEET 1 AA1 2 VAL A 134 ASP A 136 0 SHEET 2 AA1 2 VAL A 143 THR A 144 -1 O VAL A 143 N VAL A 135 CISPEP 1 ASN A 140 PRO A 141 0 1.68 CRYST1 65.377 98.891 49.970 90.00 90.00 90.00 C 2 2 21 8 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 0.015296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020012 0.00000