HEADER TRANSFERASE 12-APR-25 9UGK TITLE CRYSTAL STRUCTURE OF RV0866 FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MPT SYNTHASE SUBUNIT 2 2,MOLYBDENUM COFACTOR BIOSYNTHESIS COMPND 5 PROTEIN E 2,MOLYBDOPTERIN-CONVERTING FACTOR LARGE SUBUNIT 2, COMPND 6 MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2 2; COMPND 7 EC: 2.8.1.12; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT 2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 GENE: MOAE2, RV0866, MTV043.59; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MOLYBDOPTERIN SYNTHASE, MOAE2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHO,B.S.KANG REVDAT 1 11-FEB-26 9UGK 0 JRNL AUTH H.J.CHO,S.H.YANG,H.S.LEE,B.S.KANG JRNL TITL STRUCTURAL COMPARISON OF THREE MOAE PROTEINS IN JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS: INSIGHTS INTO MOLYBDOPTERIN JRNL TITL 3 SYNTHASE ASSEMBLY AND SPECIFICITY. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 768 51945 2025 JRNL REFN ESSN 1090-2104 JRNL PMID 40345009 JRNL DOI 10.1016/J.BBRC.2025.151945 REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 13477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 29.0000 - 4.7305 1.00 1325 148 0.2103 0.2474 REMARK 3 2 4.7305 - 3.7573 1.00 1248 139 0.1774 0.2069 REMARK 3 3 3.7573 - 3.2831 1.00 1241 136 0.1840 0.2309 REMARK 3 4 3.2831 - 2.9832 1.00 1221 137 0.2021 0.2249 REMARK 3 5 2.9832 - 2.7696 1.00 1217 135 0.2129 0.2368 REMARK 3 6 2.7696 - 2.6064 1.00 1217 135 0.2138 0.2623 REMARK 3 7 2.6064 - 2.4760 1.00 1196 133 0.2282 0.2825 REMARK 3 8 2.4760 - 2.3682 1.00 1207 134 0.2316 0.2865 REMARK 3 9 2.3682 - 2.2771 0.98 1177 130 0.2425 0.3241 REMARK 3 10 2.2400 - 2.2000 0.91 1081 120 0.2384 0.2812 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.910 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 : 0.001 2196 REMARK 3 ANGLE : 0.380 2981 REMARK 3 CHIRALITY : 0.040 343 REMARK 3 PLANARITY : 0.002 391 REMARK 3 DIHEDRAL : 2.029 1519 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 9UGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300058470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 : 11.80 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.04200 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: 2WP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD,10% DIOXANE, 0.1M HEPES PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.20950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.07550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.69400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.07550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.20950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.69400 REMARK 290 SMTRY3 4 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: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY B 139 REMARK 465 SER B 140 REMARK 465 VAL B 141 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 GLU B 136 CG CD 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 ALA B 7 58.69 -146.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 9UGK A 1 141 UNP P9WJR1 MOAE2_MYCTU 1 141 DBREF 9UGK B 1 141 UNP P9WJR1 MOAE2_MYCTU 1 141 SEQADV 9UGK GLY A -3 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK ALA A -2 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK MET A -1 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK ALA A 0 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK GLY B -3 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK ALA B -2 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK MET B -1 UNP P9WJR1 EXPRESSION TAG SEQADV 9UGK ALA B 0 UNP P9WJR1 EXPRESSION TAG SEQRES 1 A 145 GLY ALA MET ALA MET THR GLN VAL LEU ARG ALA ALA LEU SEQRES 2 A 145 THR ASP GLN PRO ILE PHE LEU ALA GLU HIS GLU GLU LEU SEQRES 3 A 145 VAL SER HIS ARG SER ALA GLY ALA ILE VAL GLY PHE VAL SEQRES 4 A 145 GLY MET ILE ARG ASP ARG ASP GLY GLY ARG GLY VAL LEU SEQRES 5 A 145 ARG LEU GLU TYR SER ALA HIS PRO SER ALA ALA GLN VAL SEQRES 6 A 145 LEU ALA ASP LEU VAL ALA GLU VAL ALA GLU GLU SER SER SEQRES 7 A 145 GLY VAL ARG ALA VAL ALA ALA SER HIS ARG ILE GLY VAL SEQRES 8 A 145 LEU GLN VAL GLY GLU ALA ALA LEU VAL ALA ALA VAL ALA SEQRES 9 A 145 ALA ASP HIS ARG ARG ALA ALA PHE GLY THR CYS ALA HIS SEQRES 10 A 145 LEU VAL GLU THR ILE LYS ALA ARG LEU PRO VAL TRP LYS SEQRES 11 A 145 HIS GLN PHE PHE GLU ASP GLY THR ASP GLU TRP VAL GLY SEQRES 12 A 145 SER VAL SEQRES 1 B 145 GLY ALA MET ALA MET THR GLN VAL LEU ARG ALA ALA LEU SEQRES 2 B 145 THR ASP GLN PRO ILE PHE LEU ALA GLU HIS GLU GLU LEU SEQRES 3 B 145 VAL SER HIS ARG SER ALA GLY ALA ILE VAL GLY PHE VAL SEQRES 4 B 145 GLY MET ILE ARG ASP ARG ASP GLY GLY ARG GLY VAL LEU SEQRES 5 B 145 ARG LEU GLU TYR SER ALA HIS PRO SER ALA ALA GLN VAL SEQRES 6 B 145 LEU ALA ASP LEU VAL ALA GLU VAL ALA GLU GLU SER SER SEQRES 7 B 145 GLY VAL ARG ALA VAL ALA ALA SER HIS ARG ILE GLY VAL SEQRES 8 B 145 LEU GLN VAL GLY GLU ALA ALA LEU VAL ALA ALA VAL ALA SEQRES 9 B 145 ALA ASP HIS ARG ARG ALA ALA PHE GLY THR CYS ALA HIS SEQRES 10 B 145 LEU VAL GLU THR ILE LYS ALA ARG LEU PRO VAL TRP LYS SEQRES 11 B 145 HIS GLN PHE PHE GLU ASP GLY THR ASP GLU TRP VAL GLY SEQRES 12 B 145 SER VAL HET MPD A 201 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *91(H2 O) HELIX 1 AA1 PHE A 15 VAL A 23 1 9 HELIX 2 AA2 SER A 57 SER A 73 1 17 HELIX 3 AA3 HIS A 103 LEU A 122 1 20 HELIX 4 AA4 PHE B 15 VAL B 23 1 9 HELIX 5 AA5 SER B 57 SER B 73 1 17 HELIX 6 AA6 HIS B 103 LEU B 122 1 20 SHEET 1 AA1 8 GLN A 3 THR A 10 0 SHEET 2 AA1 8 VAL A 76 ARG A 84 1 O ARG A 77 N GLN A 3 SHEET 3 AA1 8 ALA A 93 ALA A 101 -1 O ALA A 100 N ALA A 78 SHEET 4 AA1 8 ALA A 30 MET A 37 -1 N GLY A 36 O ALA A 94 SHEET 5 AA1 8 ALA B 30 MET B 37 -1 O GLY B 33 N GLY A 33 SHEET 6 AA1 8 ALA B 93 ALA B 101 -1 O ALA B 94 N GLY B 36 SHEET 7 AA1 8 VAL B 76 ARG B 84 -1 N ALA B 80 O ALA B 98 SHEET 8 AA1 8 GLN B 3 THR B 10 1 N LEU B 5 O VAL B 79 SHEET 1 AA2 3 ARG A 41 ASP A 42 0 SHEET 2 AA2 3 ARG A 45 ALA A 54 -1 O ARG A 45 N ASP A 42 SHEET 3 AA2 3 GLY A 86 GLN A 89 -1 O LEU A 88 N LEU A 50 SHEET 1 AA3 4 ARG A 41 ASP A 42 0 SHEET 2 AA3 4 ARG A 45 ALA A 54 -1 O ARG A 45 N ASP A 42 SHEET 3 AA3 4 VAL A 124 PHE A 130 -1 O TRP A 125 N SER A 53 SHEET 4 AA3 4 ASP A 135 TRP A 137 -1 O GLU A 136 N GLN A 128 SHEET 1 AA4 3 ARG B 41 ASP B 42 0 SHEET 2 AA4 3 ARG B 45 ALA B 54 -1 O ARG B 45 N ASP B 42 SHEET 3 AA4 3 GLY B 86 GLN B 89 -1 O LEU B 88 N LEU B 50 SHEET 1 AA5 4 ARG B 41 ASP B 42 0 SHEET 2 AA5 4 ARG B 45 ALA B 54 -1 O ARG B 45 N ASP B 42 SHEET 3 AA5 4 VAL B 124 PHE B 130 -1 O HIS B 127 N GLU B 51 SHEET 4 AA5 4 ASP B 135 VAL B 138 -1 O VAL B 138 N LYS B 126 CRYST1 46.419 61.388 90.151 90.00 90.00 90.00 P 21 21 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 0.021543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011093 0.00000 CONECT 2153 2154 CONECT 2154 2153 2155 2156 2157 CONECT 2155 2154 CONECT 2156 2154 CONECT 2157 2154 2158 CONECT 2158 2157 2159 2160 CONECT 2159 2158 CONECT 2160 2158 MASTER 236 0 1 6 22 0 0 6 2243 2 8 24 END