HEADER TRANSCRIPTION 04-AUG-15 5D19 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RV0302, FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: ACRR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MYCOBACTERIUM TUBERCULOSIS, TRANSCRIPTIONAL REGULATOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.-H.CHOU,J.DELMAR,C.-C.SU,E.YU REVDAT 3 06-MAR-24 5D19 1 REMARK REVDAT 2 22-NOV-17 5D19 1 JRNL REMARK REVDAT 1 07-OCT-15 5D19 0 JRNL AUTH T.H.CHOU,J.A.DELMAR,C.C.WRIGHT,N.KUMAR,A.RADHAKRISHNAN, JRNL AUTH 2 J.K.DOH,M.H.LICON,J.REDDY BOLLA,H.T.LEI,K.R.RAJASHANKAR, JRNL AUTH 3 C.C.SU,G.E.PURDY,E.W.YU JRNL TITL CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 TRANSCRIPTIONAL REGULATOR RV0302. JRNL REF PROTEIN SCI. 2015 JRNL REFN ESSN 1469-896X JRNL PMID 26362239 JRNL DOI 10.1002/PRO.2802 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 12485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 609 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.52 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.370 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D19 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, K MES, SODIUM CHLORIDE, REMARK 280 ISOPROPYL ALCOHOL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 38.64900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.44400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.64900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.44400 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: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 345 LIES ON A SPECIAL POSITION. 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 GLY A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 GLN A 9 REMARK 465 GLN A 10 REMARK 465 GLN A 11 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 VAL B 3 REMARK 465 PRO B 4 REMARK 465 ALA B 5 REMARK 465 LYS B 6 REMARK 465 LYS B 7 REMARK 465 LYS B 8 REMARK 465 GLN B 9 REMARK 465 GLN B 10 REMARK 465 GLN B 11 REMARK 465 HIS B 214 REMARK 465 HIS B 215 REMARK 465 HIS B 216 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 PHE A 55 -62.49 -127.25 REMARK 500 THR B 29 -70.98 -98.00 REMARK 500 PHE B 73 -63.70 -105.91 REMARK 500 ILE B 77 50.78 38.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D18 RELATED DB: PDB DBREF1 5D19 A 1 210 UNP A0A045J2D2_MYCTX DBREF2 5D19 A A0A045J2D2 1 210 DBREF1 5D19 B 1 210 UNP A0A045J2D2_MYCTX DBREF2 5D19 B A0A045J2D2 1 210 SEQADV 5D19 HIS A 211 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS A 212 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS A 213 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS A 214 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS A 215 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS A 216 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 211 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 212 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 213 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 214 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 215 UNP A0A045J2D EXPRESSION TAG SEQADV 5D19 HIS B 216 UNP A0A045J2D EXPRESSION TAG SEQRES 1 A 216 MET GLY VAL PRO ALA LYS LYS LYS GLN GLN GLN GLY GLU SEQRES 2 A 216 ARG SER ARG GLU SER ILE LEU ASP ALA THR GLU ARG LEU SEQRES 3 A 216 MET ALA THR LYS GLY TYR ALA ALA THR SER ILE SER ASP SEQRES 4 A 216 ILE ARG ASP ALA CYS GLY LEU ALA PRO SER SER ILE TYR SEQRES 5 A 216 TRP HIS PHE GLY SER LYS GLU GLY VAL LEU ALA ALA MET SEQRES 6 A 216 MET GLU ARG GLY ALA GLN ARG PHE PHE ALA ALA ILE PRO SEQRES 7 A 216 THR TRP ASP GLU ALA HIS GLY PRO VAL GLU GLN ARG SER SEQRES 8 A 216 GLU ARG GLN LEU THR GLU LEU VAL SER LEU GLN SER GLN SEQRES 9 A 216 HIS PRO ASP PHE LEU ARG LEU PHE TYR LEU LEU SER MET SEQRES 10 A 216 GLU ARG SER GLN ASP PRO ALA VAL ALA ALA VAL VAL ARG SEQRES 11 A 216 ARG VAL ARG ASN THR ALA ILE ALA ARG PHE ARG ASP SER SEQRES 12 A 216 ILE THR HIS LEU LEU PRO SER ASP ILE PRO PRO GLY LYS SEQRES 13 A 216 ALA ASP LEU VAL VAL ALA GLU LEU THR ALA PHE ALA VAL SEQRES 14 A 216 ALA LEU SER ASP GLY VAL TYR PHE ALA GLY HIS LEU GLU SEQRES 15 A 216 PRO ASP THR THR ASP VAL GLU ARG MET TYR ARG ARG LEU SEQRES 16 A 216 ARG GLN ALA LEU GLU ALA LEU ILE PRO VAL LEU LEU GLU SEQRES 17 A 216 GLU THR HIS HIS HIS HIS HIS HIS SEQRES 1 B 216 MET GLY VAL PRO ALA LYS LYS LYS GLN GLN GLN GLY GLU SEQRES 2 B 216 ARG SER ARG GLU SER ILE LEU ASP ALA THR GLU ARG LEU SEQRES 3 B 216 MET ALA THR LYS GLY TYR ALA ALA THR SER ILE SER ASP SEQRES 4 B 216 ILE ARG ASP ALA CYS GLY LEU ALA PRO SER SER ILE TYR SEQRES 5 B 216 TRP HIS PHE GLY SER LYS GLU GLY VAL LEU ALA ALA MET SEQRES 6 B 216 MET GLU ARG GLY ALA GLN ARG PHE PHE ALA ALA ILE PRO SEQRES 7 B 216 THR TRP ASP GLU ALA HIS GLY PRO VAL GLU GLN ARG SER SEQRES 8 B 216 GLU ARG GLN LEU THR GLU LEU VAL SER LEU GLN SER GLN SEQRES 9 B 216 HIS PRO ASP PHE LEU ARG LEU PHE TYR LEU LEU SER MET SEQRES 10 B 216 GLU ARG SER GLN ASP PRO ALA VAL ALA ALA VAL VAL ARG SEQRES 11 B 216 ARG VAL ARG ASN THR ALA ILE ALA ARG PHE ARG ASP SER SEQRES 12 B 216 ILE THR HIS LEU LEU PRO SER ASP ILE PRO PRO GLY LYS SEQRES 13 B 216 ALA ASP LEU VAL VAL ALA GLU LEU THR ALA PHE ALA VAL SEQRES 14 B 216 ALA LEU SER ASP GLY VAL TYR PHE ALA GLY HIS LEU GLU SEQRES 15 B 216 PRO ASP THR THR ASP VAL GLU ARG MET TYR ARG ARG LEU SEQRES 16 B 216 ARG GLN ALA LEU GLU ALA LEU ILE PRO VAL LEU LEU GLU SEQRES 17 B 216 GLU THR HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *79(H2 O) HELIX 1 AA1 GLY A 12 LYS A 30 1 19 HELIX 2 AA2 SER A 36 GLY A 45 1 10 HELIX 3 AA3 ALA A 47 PHE A 55 1 9 HELIX 4 AA4 SER A 57 ALA A 76 1 20 HELIX 5 AA5 GLN A 89 HIS A 105 1 17 HELIX 6 AA6 PRO A 106 MET A 117 1 12 HELIX 7 AA7 ASP A 122 LEU A 147 1 26 HELIX 8 AA8 PRO A 153 GLU A 182 1 30 HELIX 9 AA9 ASP A 187 THR A 210 1 24 HELIX 10 AB1 ARG B 14 LYS B 30 1 17 HELIX 11 AB2 SER B 36 GLY B 45 1 10 HELIX 12 AB3 ALA B 47 PHE B 55 1 9 HELIX 13 AB4 SER B 57 PHE B 74 1 18 HELIX 14 AB5 TRP B 80 GLY B 85 1 6 HELIX 15 AB6 GLU B 88 GLN B 104 1 17 HELIX 16 AB7 PRO B 106 GLU B 118 1 13 HELIX 17 AB8 ASP B 122 HIS B 146 1 25 HELIX 18 AB9 PRO B 153 GLU B 182 1 30 HELIX 19 AC1 ASP B 187 THR B 210 1 24 CRYST1 77.298 118.888 46.220 90.00 90.00 90.00 P 21 21 2 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 0.012937 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021636 0.00000