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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 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. 2014
JRNL REFN ESSN 1083-351X
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
TER 2237 GLY A 282
MASTER 262 0 1 12 8 0 0 6 2489 1 18 24
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