HEADER TRANSCRIPTION 13-AUG-14 4W1U TITLE CRYSTAL STRUCTURE OF RV3557C/KSTR2, A TRANSCRIPTIONAL REPRESSOR TITLE 2 INVOLVED IN CHOLESTEROL METABOLISM IN MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: KSTR2, RV3557C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS TETR-FAMILY REPRESSOR, CHOLESTEROL, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.S.DAWES,S.K.KENDALL,E.N.BAKER,J.S.LOTT REVDAT 3 27-SEP-23 4W1U 1 REMARK REVDAT 2 22-NOV-17 4W1U 1 SOURCE REMARK REVDAT 1 29-JUL-15 4W1U 0 JRNL AUTH S.S.DAWES,S.K.KENDALL,E.N.BAKER,J.S.LOTT JRNL TITL CRYSTAL STRUCTURE OF RV3557C/KSTR2, A TRANSCRIPTIONAL JRNL TITL 2 REPRESSOR INVOLVED IN CHOLESTEROL METABOLISM IN JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 19811 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1008 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 26.6030 - 3.5837 0.98 2769 163 0.1601 0.1788 REMARK 3 2 3.5837 - 2.8455 0.98 2768 139 0.1679 0.1908 REMARK 3 3 2.8455 - 2.4862 0.97 2685 153 0.1813 0.2090 REMARK 3 4 2.4862 - 2.2590 0.96 2697 138 0.1722 0.2297 REMARK 3 5 2.2590 - 2.0971 0.96 2685 144 0.1685 0.1921 REMARK 3 6 2.0971 - 1.9735 0.95 2624 141 0.1841 0.2418 REMARK 3 7 1.9735 - 1.8750 0.93 2575 130 0.2283 0.2775 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.57 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 1632 REMARK 3 ANGLE : 0.926 2222 REMARK 3 CHIRALITY : 0.039 238 REMARK 3 PLANARITY : 0.005 294 REMARK 3 DIHEDRAL : 14.895 608 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.4007 -2.3122 54.7595 REMARK 3 T TENSOR REMARK 3 T11: 0.4036 T22: 0.3468 REMARK 3 T33: 0.3241 T12: 0.0342 REMARK 3 T13: 0.1227 T23: -0.0639 REMARK 3 L TENSOR REMARK 3 L11: 5.4723 L22: 7.1839 REMARK 3 L33: 2.0166 L12: -2.7086 REMARK 3 L13: 7.4768 L23: -3.8864 REMARK 3 S TENSOR REMARK 3 S11: -0.1138 S12: -0.4591 S13: 0.1902 REMARK 3 S21: 0.4309 S22: -0.0432 S23: 0.3491 REMARK 3 S31: -0.3270 S32: -0.3366 S33: 0.1343 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 35 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.6861 -16.9326 46.8057 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.2123 REMARK 3 T33: 0.1251 T12: -0.0196 REMARK 3 T13: -0.0218 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.0272 L22: 7.0604 REMARK 3 L33: 0.8528 L12: 0.9312 REMARK 3 L13: 0.0880 L23: 1.3983 REMARK 3 S TENSOR REMARK 3 S11: 0.1058 S12: -0.1655 S13: 0.0987 REMARK 3 S21: 0.4156 S22: -0.0438 S23: -0.2472 REMARK 3 S31: -0.0108 S32: 0.0265 S33: -0.0640 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 151 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.3747 -28.2856 42.9899 REMARK 3 T TENSOR REMARK 3 T11: 0.0524 T22: 0.1654 REMARK 3 T33: 0.1175 T12: -0.0080 REMARK 3 T13: -0.0294 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 4.4184 L22: 6.3155 REMARK 3 L33: 7.1186 L12: -0.3830 REMARK 3 L13: -0.9116 L23: 1.8251 REMARK 3 S TENSOR REMARK 3 S11: 0.2057 S12: -0.2549 S13: 0.2117 REMARK 3 S21: 0.1867 S22: -0.1635 S23: 0.2028 REMARK 3 S31: -0.1974 S32: 0.0714 S33: -0.0829 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 4W1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000201898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 203 REMARK 200 PH : 4.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19815 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 48.113 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 FOR SHELL : 4.400 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: PDB ENTRY 2IBD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CITRIC ACID, 14% MPEG 5000, PH REMARK 280 4.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.17800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.14600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.17800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.14600 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: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 83.23723 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.09245 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 A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLY A 6 REMARK 465 GLN A 7 REMARK 465 VAL A 8 REMARK 465 ASN A 9 REMARK 465 SER A 10 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 ARG A 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 12 NE CZ NH1 NH2 REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 173 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 198 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 306 O HOH A 340 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 4W1U A 1 200 UNP P9WMB9 KSTR2_MYCTU 1 200 SEQADV 4W1U GLY A -3 UNP P9WMB9 EXPRESSION TAG SEQADV 4W1U ALA A -2 UNP P9WMB9 EXPRESSION TAG SEQADV 4W1U MET A -1 UNP P9WMB9 EXPRESSION TAG SEQADV 4W1U GLY A 0 UNP P9WMB9 EXPRESSION TAG SEQRES 1 A 204 GLY ALA MET GLY MET ASP ARG VAL ALA GLY GLN VAL ASN SEQRES 2 A 204 SER ARG ARG GLY GLU LEU LEU GLU LEU ALA ALA ALA MET SEQRES 3 A 204 PHE ALA GLU ARG GLY LEU ARG ALA THR THR VAL ARG ASP SEQRES 4 A 204 ILE ALA ASP GLY ALA GLY ILE LEU SER GLY SER LEU TYR SEQRES 5 A 204 HIS HIS PHE ALA SER LYS GLU GLU MET VAL ASP GLU LEU SEQRES 6 A 204 LEU ARG GLY PHE LEU ASP TRP LEU PHE ALA ARG TYR ARG SEQRES 7 A 204 ASP ILE VAL ASP SER THR ALA ASN PRO LEU GLU ARG LEU SEQRES 8 A 204 GLN GLY LEU PHE MET ALA SER PHE GLU ALA ILE GLU HIS SEQRES 9 A 204 HIS HIS ALA GLN VAL VAL ILE TYR GLN ASP GLU ALA GLN SEQRES 10 A 204 ARG LEU ALA SER GLN PRO ARG PHE SER TYR ILE GLU ASP SEQRES 11 A 204 ARG ASN LYS GLN GLN ARG LYS MET TRP VAL ASP VAL LEU SEQRES 12 A 204 ASN GLN GLY ILE GLU GLU GLY TYR PHE ARG PRO ASP LEU SEQRES 13 A 204 ASP VAL ASP LEU VAL TYR ARG PHE ILE ARG ASP THR THR SEQRES 14 A 204 TRP VAL SER VAL ARG TRP TYR ARG PRO GLY GLY PRO LEU SEQRES 15 A 204 THR ALA GLN GLN VAL GLY GLN GLN TYR LEU ALA ILE VAL SEQRES 16 A 204 LEU GLY GLY ILE THR LYS GLU GLY VAL FORMUL 2 HOH *158(H2 O) HELIX 1 AA1 ARG A 12 GLY A 27 1 16 HELIX 2 AA2 THR A 32 ALA A 40 1 9 HELIX 3 AA3 LEU A 43 TYR A 48 1 6 HELIX 4 AA4 SER A 53 THR A 80 1 28 HELIX 5 AA5 ASN A 82 HIS A 101 1 20 HELIX 6 AA6 HIS A 101 ALA A 116 1 16 HELIX 7 AA7 SER A 117 PHE A 121 5 5 HELIX 8 AA8 SER A 122 GLU A 145 1 24 HELIX 9 AA9 ASP A 153 VAL A 167 1 15 HELIX 10 AB1 SER A 168 TRP A 171 5 4 HELIX 11 AB2 THR A 179 GLY A 194 1 16 CRYST1 72.356 90.292 49.693 90.00 128.21 90.00 C 1 2 1 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 0.013820 0.000000 0.010878 0.00000 SCALE2 0.000000 0.011075 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025609 0.00000