HEADER TRANSCRIPTION 12-MAR-13 4JKZ TITLE CRYSTAL STRUCTURE OF MS6564 FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, TETR FAMILY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATOR, TETR FAMILY PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_6564, MSMEI_6387; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TRANSCRIPTIONAL REGULATOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.F.YANG,Z.Q.GAO,Z.G.HE,Y.H.DONG REVDAT 4 28-FEB-24 4JKZ 1 REMARK REVDAT 3 24-AUG-22 4JKZ 1 JRNL SEQADV REVDAT 2 15-NOV-17 4JKZ 1 REMARK REVDAT 1 26-JUN-13 4JKZ 0 JRNL AUTH S.YANG,Z.GAO,T.LI,M.YANG,T.ZHANG,Y.DONG,Z.G.HE JRNL TITL STRUCTURAL BASIS FOR INTERACTION BETWEEN MYCOBACTERIUM JRNL TITL 2 SMEGMATIS MS6564, A TETR FAMILY MASTER REGULATOR, AND ITS JRNL TITL 3 TARGET DNA. JRNL REF J.BIOL.CHEM. V. 288 23687 2013 JRNL REFN ESSN 1083-351X JRNL PMID 23803605 JRNL DOI 10.1074/JBC.M113.468694 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16361 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 824 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 29.5762 - 3.2692 1.00 2741 118 0.2017 0.2515 REMARK 3 2 3.2692 - 2.5953 1.00 2595 159 0.2219 0.2676 REMARK 3 3 2.5953 - 2.2674 1.00 2572 149 0.2052 0.2470 REMARK 3 4 2.2674 - 2.0602 1.00 2572 131 0.2064 0.2638 REMARK 3 5 2.0602 - 1.9125 1.00 2560 129 0.2359 0.2920 REMARK 3 6 1.9125 - 1.8000 0.98 2497 138 0.2739 0.3376 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.550 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) : 18.38990 REMARK 3 B22 (A**2) : 9.67970 REMARK 3 B33 (A**2) : 13.57990 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1378 REMARK 3 ANGLE : 1.048 1865 REMARK 3 CHIRALITY : 0.066 220 REMARK 3 PLANARITY : 0.004 242 REMARK 3 DIHEDRAL : 14.869 509 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 4JKZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078177. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-12 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 : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CITRATE, 0.1M HEPES, 30% REMARK 280 MPD, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 24.99200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.99200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.13150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.14450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.13150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.14450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.99200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.13150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.14450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 24.99200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.13150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.14450 REMARK 290 SMTRY3 8 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: 2630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 -58.26300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 24.99200 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 HIS A -4 REMARK 465 MET A -3 REMARK 465 ALA A -2 REMARK 465 SER A -1 REMARK 465 MET A 0 REMARK 465 THR A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 MET A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 8 REMARK 465 ARG A 9 REMARK 465 ARG A 10 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 NE2 HIS A 148 O HOH A 240 2.15 REMARK 500 O HOH A 249 O HOH A 253 2.16 REMARK 500 O HOH A 286 O HOH A 293 2.18 REMARK 500 O HOH A 212 O HOH A 217 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 12 -13.85 -146.17 REMARK 500 GLU A 28 -43.20 -163.84 REMARK 500 LEU A 34 79.77 -153.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JL3 RELATED DB: PDB DBREF 4JKZ A 8 189 UNP A0R6I8 A0R6I8_MYCS2 8 189 SEQADV 4JKZ HIS A -4 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ MET A -3 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ ALA A -2 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ SER A -1 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ MET A 0 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ THR A 1 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ GLY A 2 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ GLY A 3 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ GLN A 4 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ GLN A 5 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ MET A 6 UNP A0R6I8 EXPRESSION TAG SEQADV 4JKZ GLY A 7 UNP A0R6I8 EXPRESSION TAG SEQRES 1 A 194 HIS MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG SEQRES 2 A 194 ARG ARG SER GLU LYS SER ARG VAL ALA ILE VAL GLU ALA SEQRES 3 A 194 THR ARG ALA LEU LEU LEU GLU ARG GLY PHE ASP GLY LEU SEQRES 4 A 194 SER ILE GLU ALA VAL ALA ALA LYS ALA GLY VAL GLY LYS SEQRES 5 A 194 GLN THR ILE TYR ARG TRP TRP PRO SER ARG HIS ALA LEU SEQRES 6 A 194 VAL ALA ASP VAL LEU LEU GLU ASP ALA ASP LYS ILE LEU SEQRES 7 A 194 ALA ARG MET PRO LYS THR ASP ASP VAL THR ALA ASP LEU SEQRES 8 A 194 ALA SER TRP ALA GLY THR LEU ALA ALA ALA LEU THR THR SEQRES 9 A 194 ARG ARG GLY HIS ALA MET LEU LYS THR LEU MET ALA ALA SEQRES 10 A 194 SER LEU GLU HIS GLU ASP THR ALA ALA ARG LEU ARG GLU SEQRES 11 A 194 GLY PHE SER ARG PRO LEU ILE GLU SER VAL ARG ASP ARG SEQRES 12 A 194 LEU ARG ASP GLU ASP ILE ASP ALA ASP HIS ALA GLN ALA SEQRES 13 A 194 ALA ALA ASP ALA LEU LEU GLY ALA VAL VAL ASN ALA VAL SEQRES 14 A 194 LEU SER GLU GLY ARG SER TYR SER ARG GLN ARG ALA GLU SEQRES 15 A 194 THR SER ALA ARG ILE ILE VAL ALA GLY LEU ARG PRO FORMUL 2 HOH *107(H2 O) HELIX 1 1 LYS A 13 GLY A 30 1 18 HELIX 2 2 SER A 35 GLY A 44 1 10 HELIX 3 3 GLY A 46 TYR A 51 1 6 HELIX 4 4 SER A 56 GLU A 67 1 12 HELIX 5 5 ASP A 68 LEU A 73 1 6 HELIX 6 6 ASP A 81 THR A 98 1 18 HELIX 7 7 THR A 99 LEU A 114 1 16 HELIX 8 8 HIS A 116 PHE A 127 1 12 HELIX 9 9 PHE A 127 ASP A 141 1 15 HELIX 10 10 ASP A 145 GLY A 168 1 24 HELIX 11 11 ARG A 169 TYR A 171 5 3 HELIX 12 12 SER A 172 GLY A 186 1 15 CISPEP 1 ARG A 188 PRO A 189 0 -6.23 CRYST1 58.263 118.289 49.984 90.00 90.00 90.00 C 2 2 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 0.017164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020006 0.00000