HEADER TRANSCRIPTION 20-JUL-06 2DU9 TITLE CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL FACTOR FROM C.GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PREDICTED TRANSCRIPTIONAL REGULATORS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTION FACTOR, BACTERIAL REGULATORY PROTEIN, GNTR COMPND 5 FAMILY; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM ATCC 13032; SOURCE 3 ORGANISM_TAXID: 196627; SOURCE 4 STRAIN: ATCC13032; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS WINGED HELIX-TURN-HELIX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.GAO,M.YAO,I.TANAKA REVDAT 5 20-NOV-24 2DU9 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2DU9 1 VERSN REVDAT 3 24-FEB-09 2DU9 1 VERSN REVDAT 2 18-SEP-07 2DU9 1 JRNL KEYWDS REVDAT 1 24-JUL-07 2DU9 0 JRNL AUTH Y.GAO,M.YAO,H.ITOU,Y.ZHOU,I.TANAKA JRNL TITL THE STRUCTURES OF TRANSCRIPTION FACTOR CGL2947 FROM JRNL TITL 2 CORYNEBACTERIUM GLUTAMICUM IN TWO CRYSTAL FORMS: A NOVEL JRNL TITL 3 HOMODIMER ASSEMBLING AND THE IMPLICATION FOR JRNL TITL 4 EFFECTOR-BINDING MODE JRNL REF PROTEIN SCI. V. 16 1878 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17766384 JRNL DOI 10.1110/PS.072976907 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.28 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) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 8143 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) : 0.265 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 798 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3295 REMARK 3 BIN FREE R VALUE : 0.3817 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 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 : 890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14700 REMARK 3 B22 (A**2) : -0.14700 REMARK 3 B33 (A**2) : 0.29300 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.34 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) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.569 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.69 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.933 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 2DU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000025850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790, 0.9793, 0.9000 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : 0.38700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 57.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 12% 2-METHYL-2,4 REMARK 280 PENTANEDIOL, 0.1M LI2SO4, PH 8.5, 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 76.24000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.47500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.12000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.47500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.47500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 114.36000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.47500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.47500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.12000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.47500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.47500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 114.36000 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 76.24000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMODIMER GENERATED FROM THE REMARK 300 MONOMER BY THE TWO FOLD AXIS:-Y+2, -X+2, -Z+1/2 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 0.000000 -1.000000 0.000000 93.90000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 93.90000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 76.24000 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 THR A 2 REMARK 465 LEU A 119 REMARK 465 TYR A 120 REMARK 465 LYS A 121 REMARK 465 LEU A 122 REMARK 465 GLU A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 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 37 -81.24 -54.20 REMARK 500 ARG A 39 70.56 -111.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 130 DBREF 2DU9 A 1 121 UNP Q8NLJ5 Q8NLJ5_CORGL 1 121 SEQADV 2DU9 MSE A 66 UNP Q8NLJ5 MET 66 MODIFIED RESIDUE SEQADV 2DU9 LEU A 122 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 GLU A 123 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 124 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 125 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 126 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 127 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 128 UNP Q8NLJ5 EXPRESSION TAG SEQADV 2DU9 HIS A 129 UNP Q8NLJ5 EXPRESSION TAG SEQRES 1 A 129 MET THR VAL PRO LEU TYR LYS GLN ILE ALA SER LEU ILE SEQRES 2 A 129 GLU ASP SER ILE VAL ASP GLY THR LEU SER ILE ASP GLN SEQRES 3 A 129 ARG VAL PRO SER THR ASN GLU LEU ALA ALA PHE HIS ARG SEQRES 4 A 129 ILE ASN PRO ALA THR ALA ARG ASN GLY LEU THR LEU LEU SEQRES 5 A 129 VAL GLU ALA GLY ILE LEU TYR LYS LYS ARG GLY ILE GLY SEQRES 6 A 129 MSE PHE VAL SER ALA GLN ALA PRO ALA LEU ILE ARG GLU SEQRES 7 A 129 ARG ARG ASP ALA ALA PHE ALA ALA THR TYR VAL ALA PRO SEQRES 8 A 129 LEU ILE ASP GLU SER ILE HIS LEU GLY PHE THR ARG ALA SEQRES 9 A 129 ARG ILE HIS ALA LEU LEU ASP GLN VAL ALA GLU SER ARG SEQRES 10 A 129 GLY LEU TYR LYS LEU GLU HIS HIS HIS HIS HIS HIS MODRES 2DU9 MSE A 66 MET SELENOMETHIONINE HET MSE A 66 8 HET MPD A 130 8 HETNAM MSE SELENOMETHIONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 MPD C6 H14 O2 FORMUL 3 HOH *47(H2 O) HELIX 1 1 PRO A 4 ASP A 19 1 16 HELIX 2 2 SER A 30 HIS A 38 1 9 HELIX 3 3 ASN A 41 ALA A 55 1 15 HELIX 4 4 GLN A 71 VAL A 89 1 19 HELIX 5 5 VAL A 89 LEU A 99 1 11 HELIX 6 6 THR A 102 ARG A 117 1 16 SHEET 1 A 3 ARG A 27 VAL A 28 0 SHEET 2 A 3 GLY A 65 VAL A 68 -1 O MSE A 66 N VAL A 28 SHEET 3 A 3 LEU A 58 LYS A 61 -1 N TYR A 59 O PHE A 67 LINK C GLY A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N PHE A 67 1555 1555 1.32 SITE 1 AC1 6 ILE A 93 SER A 96 PHE A 101 ARG A 103 SITE 2 AC1 6 LEU A 110 ALA A 114 CRYST1 46.950 46.950 152.480 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 0.021299 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006558 0.00000