HEADER TRANSCRIPTION 13-NOV-07 2ZCX TITLE CRYSTAL STRUCTURE OF TETR FAMILY TRANSCRIPTIONAL REGULATOR SCO7815 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR-FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCO7815; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 1902; SOURCE 4 STRAIN: A3(2); SOURCE 5 GENE: SCO7815; SOURCE 6 EXPRESSION_SYSTEM: RHODOCOCCUS ERYTHROPOLIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1833; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: L88; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTIP KEYWDS TETR FAMILY, HELIX-TURN-HELIX, DNA-BINDING, TRANSCRIPTION REGULATION, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR U.OKADA,K.KONDO,M.YAO,N.WATANABE,I.TANAKA REVDAT 3 13-MAR-24 2ZCX 1 SEQADV REVDAT 2 24-FEB-09 2ZCX 1 VERSN REVDAT 1 18-NOV-08 2ZCX 0 JRNL AUTH U.OKADA,K.KONDO,T.HAYASHI,N.WATANABE,M.YAO,T.TAMURA,I.TANAKA JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF TETR FAMILY JRNL TITL 2 TRANSCRIPTIONAL REGULATOR SCO7815 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 616 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.91 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.86600 REMARK 3 B22 (A**2) : -0.86600 REMARK 3 B33 (A**2) : 1.73100 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.170 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.29 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.738 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000027813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.29 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12269 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 27.00 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.7050 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : 0.43000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.064 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M POTASSIUM SODIUM TARTRATE, 0.1M REMARK 280 TRIS-HCL, 1% PEG5000MME, PH8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.21200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.03400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.03400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.60600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.03400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.03400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.81800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.03400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.03400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.60600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.03400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.03400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.81800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.21200 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: 4530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.9 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 346 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 348 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 PRO A 2 REMARK 465 TYR A 3 REMARK 465 ASP A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 MET A 7 REMARK 465 THR A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 PHE A 12 REMARK 465 GLN A 13 REMARK 465 ARG A 14 REMARK 465 ALA A 15 REMARK 465 ARG A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 LEU A 224 REMARK 465 GLU A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 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 ARG A 42 15.47 -63.48 REMARK 500 GLU A 43 10.11 -151.30 REMARK 500 ALA A 96 5.21 171.65 REMARK 500 ARG A 128 -14.76 -161.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED DBREF 2ZCX A 1 223 UNP Q9FBX0 Q9FBX0_STRCO 1 223 SEQADV 2ZCX LEU A 224 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX GLU A 225 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 226 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 227 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 228 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 229 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 230 UNP Q9FBX0 EXPRESSION TAG SEQADV 2ZCX HIS A 231 UNP Q9FBX0 EXPRESSION TAG SEQRES 1 A 231 MET PRO TYR ASP ASP VAL MET THR GLY SER GLY PHE GLN SEQRES 2 A 231 ARG ALA ARG SER ALA GLN ALA LYS GLN GLN ARG GLU GLU SEQRES 3 A 231 ALA ILE LEU ASP ALA ALA ARG GLU LEU GLY THR GLU ARG SEQRES 4 A 231 GLY ILE ARG GLU ILE THR LEU THR ASP ILE ALA ALA THR SEQRES 5 A 231 VAL GLY MET HIS LYS SER ALA LEU LEU ARG TYR PHE GLU SEQRES 6 A 231 THR ARG GLU GLN ILE PHE LEU LYS ILE THR ALA GLU GLY SEQRES 7 A 231 TRP LYS GLU TRP SER ALA GLU LEU CYS ALA ARG LEU ARG SEQRES 8 A 231 GLU LEU PRO GLY ALA ALA PRO ASP ALA VAL GLY GLN VAL SEQRES 9 A 231 PHE ALA ALA THR LEU ALA ALA ARG PRO LEU PHE CYS ASP SEQRES 10 A 231 LEU LEU ALA GLN ALA PRO LEU ASN LEU GLU ARG ASN VAL SEQRES 11 A 231 SER VAL GLU SER VAL ARG SER PHE LYS ILE ALA THR LEU SEQRES 12 A 231 ASP GLU VAL GLY ARG ILE GLY ALA GLU LEU ARG ARG LEU SEQRES 13 A 231 LEU GLY VAL ASP GLU THR GLN ALA VAL ASP VAL ILE ALA SEQRES 14 A 231 THR ALA THR SER LEU ALA GLY ALA LEU TRP GLN MET ALA SEQRES 15 A 231 THR PRO GLY PRO HIS ILE GLN THR LEU TYR ARG SER ASP SEQRES 16 A 231 PRO ARG LEU ALA HIS ALA VAL VAL GLU VAL GLU PRO ARG SEQRES 17 A 231 LEU ASN ARG VAL LEU GLY ALA LEU LEU ARG GLY ILE ALA SEQRES 18 A 231 ASP GLY LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *120(H2 O) HELIX 1 1 GLN A 22 ARG A 39 1 18 HELIX 2 2 LEU A 46 VAL A 53 1 8 HELIX 3 3 LYS A 57 TYR A 63 1 7 HELIX 4 4 ARG A 67 LEU A 90 1 24 HELIX 5 5 PRO A 98 ALA A 110 1 13 HELIX 6 6 ARG A 112 ASN A 125 1 14 HELIX 7 7 VAL A 132 LEU A 157 1 26 HELIX 8 8 GLU A 161 ALA A 182 1 22 HELIX 9 9 PRO A 186 SER A 194 1 9 HELIX 10 10 PRO A 196 ALA A 201 5 6 HELIX 11 11 VAL A 205 ALA A 221 1 17 CRYST1 72.068 72.068 90.424 90.00 90.00 90.00 P 41 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 0.013876 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011059 0.00000