HEADER TRANSFERASE 14-MAY-14 4QDU TITLE CRYSTAL STRUCTURE OF ANTIGEN 85C CO-CRYSTALLIZED WITH EBSELEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIACYLGLYCEROL ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 46-340; COMPND 5 SYNONYM: DGAT, ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE, ANTIGEN 85 COMPND 6 COMPLEX C, 85C, AG85C, FIBRONECTIN-BINDING PROTEIN C, FBPS C; COMPND 7 EC: 2.3.1.122, 2.3.1.20; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: FBPC, MPT45, MTCI5.03C, RV0129C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA/BETA-HYDROLASE FOLD, MYCOLYLTRANSFERASE, DIACYLGLYCEROL KEYWDS 2 ACYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.FAVROT,D.H.LAJINESS,D.R.RONNING REVDAT 3 24-SEP-14 4QDU 1 JRNL REVDAT 2 30-JUL-14 4QDU 1 JRNL REVDAT 1 09-JUL-14 4QDU 0 JRNL AUTH L.FAVROT,D.H.LAJINESS,D.R.RONNING JRNL TITL INACTIVATION OF THE MYCOBACTERIUM TUBERCULOSIS ANTIGEN 85 JRNL TITL 2 COMPLEX BY COVALENT, ALLOSTERIC INHIBITORS. JRNL REF J.BIOL.CHEM. V. 289 25031 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 25028518 JRNL DOI 10.1074/JBC.M114.582445 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 59653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.350 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 37.6176 - 3.3732 0.95 4215 146 0.1467 0.1884 REMARK 3 2 3.3732 - 2.6776 1.00 4253 147 0.1616 0.1849 REMARK 3 3 2.6776 - 2.3392 1.00 4207 147 0.1582 0.1949 REMARK 3 4 2.3392 - 2.1254 1.00 4190 145 0.1420 0.1690 REMARK 3 5 2.1254 - 1.9730 1.00 4167 144 0.1436 0.1664 REMARK 3 6 1.9730 - 1.8567 1.00 4183 146 0.1426 0.1803 REMARK 3 7 1.8567 - 1.7637 1.00 4142 144 0.1354 0.1983 REMARK 3 8 1.7637 - 1.6869 1.00 4139 142 0.1285 0.1477 REMARK 3 9 1.6869 - 1.6220 1.00 4160 145 0.1212 0.1678 REMARK 3 10 1.6220 - 1.5660 1.00 4086 141 0.1190 0.1625 REMARK 3 11 1.5660 - 1.5171 1.00 4157 145 0.1247 0.1921 REMARK 3 12 1.5171 - 1.4737 1.00 4102 143 0.1369 0.2045 REMARK 3 13 1.4737 - 1.4349 0.97 4006 138 0.1503 0.1756 REMARK 3 14 1.4349 - 1.3999 0.88 3646 127 0.1598 0.2081 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.440 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 2315 REMARK 3 ANGLE : 1.095 3172 REMARK 3 CHIRALITY : 0.047 314 REMARK 3 PLANARITY : 0.007 423 REMARK 3 DIHEDRAL : 13.758 825 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 4QDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-14. REMARK 100 THE RCSB ID CODE IS RCSB085929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07818 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : 0.30400 REMARK 200 FOR SHELL : 5.414 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M SODIUM ACETATE REMARK 280 TRIHYDRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 29.73550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.60400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.89300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.60400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.73550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.89300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A -1 REMARK 465 ALA A 283 REMARK 465 THR A 284 REMARK 465 PRO A 285 REMARK 465 PRO A 286 REMARK 465 ALA A 287 REMARK 465 ALA A 288 REMARK 465 PRO A 289 REMARK 465 ALA A 290 REMARK 465 ALA A 291 REMARK 465 PRO A 292 REMARK 465 ALA A 293 REMARK 465 ALA A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 465 HIS A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 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 PRO A 54 32.45 -92.48 REMARK 500 PHE A 76 19.26 55.45 REMARK 500 SER A 86 -35.10 125.81 REMARK 500 ARG A 101 -61.97 -125.20 REMARK 500 SER A 124 -123.29 49.36 REMARK 500 ASN A 152 58.85 -144.34 REMARK 500 SER A 169 75.28 -110.17 REMARK 500 ASP A 216 9.91 58.74 REMARK 500 ARG A 248 17.66 -147.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QDO RELATED DB: PDB REMARK 900 RELATED ID: 4QDT RELATED DB: PDB REMARK 900 RELATED ID: 4QDX RELATED DB: PDB REMARK 900 RELATED ID: 4QDZ RELATED DB: PDB DBREF 4QDU A 0 294 UNP P9WQN9 A85C_MYCTU 46 340 SEQADV 4QDU MET A -1 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 295 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 296 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 297 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 298 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 299 UNP P9WQN9 EXPRESSION TAG SEQADV 4QDU HIS A 300 UNP P9WQN9 EXPRESSION TAG SEQRES 1 A 302 MET ALA PHE SER ARG PRO GLY LEU PRO VAL GLU TYR LEU SEQRES 2 A 302 GLN VAL PRO SER ALA SER MET GLY ARG ASP ILE LYS VAL SEQRES 3 A 302 GLN PHE GLN GLY GLY GLY PRO HIS ALA VAL TYR LEU LEU SEQRES 4 A 302 ASP GLY LEU ARG ALA GLN ASP ASP TYR ASN GLY TRP ASP SEQRES 5 A 302 ILE ASN THR PRO ALA PHE GLU GLU TYR TYR GLN SER GLY SEQRES 6 A 302 LEU SER VAL ILE MET PRO VAL GLY GLY GLN SER SER PHE SEQRES 7 A 302 TYR THR ASP TRP TYR GLN PRO SER GLN SER ASN GLY GLN SEQRES 8 A 302 ASN TYR THR TYR LYS TRP GLU THR PHE LEU THR ARG GLU SEQRES 9 A 302 MET PRO ALA TRP LEU GLN ALA ASN LYS GLY VAL SER PRO SEQRES 10 A 302 THR GLY ASN ALA ALA VAL GLY LEU SER MET SER GLY GLY SEQRES 11 A 302 SER ALA LEU ILE LEU ALA ALA TYR TYR PRO GLN GLN PHE SEQRES 12 A 302 PRO TYR ALA ALA SER LEU SER GLY PHE LEU ASN PRO SER SEQRES 13 A 302 GLU GLY TRP TRP PRO THR LEU ILE GLY LEU ALA MET ASN SEQRES 14 A 302 ASP SER GLY GLY TYR ASN ALA ASN SER MET TRP GLY PRO SEQRES 15 A 302 SER SER ASP PRO ALA TRP LYS ARG ASN ASP PRO MET VAL SEQRES 16 A 302 GLN ILE PRO ARG LEU VAL ALA ASN ASN THR ARG ILE TRP SEQRES 17 A 302 VAL TYR 30V GLY ASN GLY THR PRO SER ASP LEU GLY GLY SEQRES 18 A 302 ASP ASN ILE PRO ALA LYS PHE LEU GLU GLY LEU THR LEU SEQRES 19 A 302 ARG THR ASN GLN THR PHE ARG ASP THR TYR ALA ALA ASP SEQRES 20 A 302 GLY GLY ARG ASN GLY VAL PHE ASN PHE PRO PRO ASN GLY SEQRES 21 A 302 THR HIS SER TRP PRO TYR TRP ASN GLU GLN LEU VAL ALA SEQRES 22 A 302 MET LYS ALA ASP ILE GLN HIS VAL LEU ASN GLY ALA THR SEQRES 23 A 302 PRO PRO ALA ALA PRO ALA ALA PRO ALA ALA HIS HIS HIS SEQRES 24 A 302 HIS HIS HIS MODRES 4QDU 30V A 209 CYS HET 30V A 209 16 HETNAM 30V S-[(2-CARBAMOYLPHENYL)SELANYL]-L-CYSTEINE FORMUL 1 30V C10 H12 N2 O3 S SE FORMUL 2 HOH *279(H2 O) HELIX 1 1 ASN A 47 THR A 53 1 7 HELIX 2 2 PRO A 54 TYR A 60 1 7 HELIX 3 3 LYS A 94 ARG A 101 1 8 HELIX 4 4 ARG A 101 GLY A 112 1 12 HELIX 5 5 SER A 124 TYR A 137 1 14 HELIX 6 6 TRP A 157 SER A 169 1 13 HELIX 7 7 ASN A 173 GLY A 179 1 7 HELIX 8 8 ASP A 183 ASN A 189 1 7 HELIX 9 9 GLN A 194 ASN A 201 1 8 HELIX 10 10 PRO A 223 ASP A 245 1 23 HELIX 11 11 SER A 261 MET A 272 1 12 HELIX 12 12 MET A 272 GLY A 282 1 11 SHEET 1 A 8 GLU A 9 SER A 15 0 SHEET 2 A 8 ARG A 20 GLN A 27 -1 O PHE A 26 N GLU A 9 SHEET 3 A 8 SER A 65 PRO A 69 -1 O MET A 68 N GLN A 25 SHEET 4 A 8 ALA A 33 LEU A 36 1 N LEU A 36 O ILE A 67 SHEET 5 A 8 ALA A 119 LEU A 123 1 O ALA A 119 N TYR A 35 SHEET 6 A 8 TYR A 143 LEU A 147 1 O ALA A 145 N ALA A 120 SHEET 7 A 8 ARG A 204 TYR A 208 1 O TYR A 208 N SER A 146 SHEET 8 A 8 GLY A 250 ASN A 253 1 O VAL A 251 N VAL A 207 LINK C TYR A 208 N 30V A 209 1555 1555 1.33 LINK C 30V A 209 N GLY A 210 1555 1555 1.33 CRYST1 59.471 67.786 75.208 90.00 90.00 90.00 P 21 21 21 4 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 0.016815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013296 0.00000