HEADER TRANSCRIPTION REGULATOR 15-MAR-05 1Z4E TITLE CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR FROM BACILLUS TITLE 2 HALODURANS C-125 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: C-125; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NYSGXRC TARGET T2017, GNAT FOLD, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, NYSGRC, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,S.C.ALMO,S.K.BURLEY,NEW YORK SGX RESEARCH AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 14-FEB-24 1Z4E 1 REMARK REVDAT 4 03-FEB-21 1Z4E 1 AUTHOR REVDAT 3 13-JUL-11 1Z4E 1 VERSN REVDAT 2 24-FEB-09 1Z4E 1 VERSN REVDAT 1 21-JUN-05 1Z4E 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR FROM BACILLUS JRNL TITL 2 HALODURANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1199444.870 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 21836 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) : 0.225 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1926 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 91 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2416 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.73000 REMARK 3 B22 (A**2) : -0.80000 REMARK 3 B33 (A**2) : 4.53000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.00 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.550 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.390 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 43.32 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z4E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-05; 15-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X9A; X9A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9610; 0.9794, 0.9792, 0.9610 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21836 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; 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 (%): 43.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, BISTRIS, LITHIUM SULFATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 36.15550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.34150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.15550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.34150 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: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 ASN A 2 REMARK 465 ILE A 3 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ILE B 3 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 ASN A 62 76.88 -119.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T2017 RELATED DB: TARGETDB DBREF 1Z4E A 1 153 UNP Q9KBG0 Q9KBG0_BACHD 1 153 DBREF 1Z4E B 1 153 UNP Q9KBG0 Q9KBG0_BACHD 1 153 SEQRES 1 A 153 MET ASN ILE HIS VAL THR ILE ARG GLU ALA THR GLU GLY SEQRES 2 A 153 ASP LEU GLU GLN MET VAL HIS MET LEU ALA ASP ASP VAL SEQRES 3 A 153 LEU GLY ARG LYS ARG GLU ARG TYR GLU LYS PRO LEU PRO SEQRES 4 A 153 VAL SER TYR VAL ARG ALA PHE LYS GLU ILE LYS LYS ASP SEQRES 5 A 153 LYS ASN ASN GLU LEU ILE VAL ALA CYS ASN GLY GLU GLU SEQRES 6 A 153 ILE VAL GLY MET LEU GLN VAL THR PHE THR PRO TYR LEU SEQRES 7 A 153 THR TYR GLN GLY SER TRP ARG ALA THR ILE GLU GLY VAL SEQRES 8 A 153 ARG THR HIS SER ALA ALA ARG GLY GLN GLY ILE GLY SER SEQRES 9 A 153 GLN LEU VAL CYS TRP ALA ILE GLU ARG ALA LYS GLU ARG SEQRES 10 A 153 GLY CYS HIS LEU ILE GLN LEU THR THR ASP LYS GLN ARG SEQRES 11 A 153 PRO ASP ALA LEU ARG PHE TYR GLU GLN LEU GLY PHE LYS SEQRES 12 A 153 ALA SER HIS GLU GLY LEU LYS MET HIS PHE SEQRES 1 B 153 MET ASN ILE HIS VAL THR ILE ARG GLU ALA THR GLU GLY SEQRES 2 B 153 ASP LEU GLU GLN MET VAL HIS MET LEU ALA ASP ASP VAL SEQRES 3 B 153 LEU GLY ARG LYS ARG GLU ARG TYR GLU LYS PRO LEU PRO SEQRES 4 B 153 VAL SER TYR VAL ARG ALA PHE LYS GLU ILE LYS LYS ASP SEQRES 5 B 153 LYS ASN ASN GLU LEU ILE VAL ALA CYS ASN GLY GLU GLU SEQRES 6 B 153 ILE VAL GLY MET LEU GLN VAL THR PHE THR PRO TYR LEU SEQRES 7 B 153 THR TYR GLN GLY SER TRP ARG ALA THR ILE GLU GLY VAL SEQRES 8 B 153 ARG THR HIS SER ALA ALA ARG GLY GLN GLY ILE GLY SER SEQRES 9 B 153 GLN LEU VAL CYS TRP ALA ILE GLU ARG ALA LYS GLU ARG SEQRES 10 B 153 GLY CYS HIS LEU ILE GLN LEU THR THR ASP LYS GLN ARG SEQRES 11 B 153 PRO ASP ALA LEU ARG PHE TYR GLU GLN LEU GLY PHE LYS SEQRES 12 B 153 ALA SER HIS GLU GLY LEU LYS MET HIS PHE FORMUL 3 HOH *146(H2 O) HELIX 1 1 THR A 11 GLY A 13 5 3 HELIX 2 2 ASP A 14 ASP A 25 1 12 HELIX 3 3 LEU A 27 ARG A 31 5 5 HELIX 4 4 PRO A 39 ASP A 52 1 14 HELIX 5 5 LEU A 78 SER A 83 1 6 HELIX 6 6 GLY A 101 ARG A 117 1 17 HELIX 7 7 ASP A 132 GLY A 141 1 10 HELIX 8 8 THR B 11 GLY B 13 5 3 HELIX 9 9 ASP B 14 ASP B 25 1 12 HELIX 10 10 LEU B 27 ARG B 31 5 5 HELIX 11 11 PRO B 39 ASP B 52 1 14 HELIX 12 12 LEU B 78 SER B 83 1 6 HELIX 13 13 GLY B 101 ARG B 117 1 17 HELIX 14 14 ASP B 132 GLN B 139 1 8 SHEET 1 A12 THR A 6 GLU A 9 0 SHEET 2 A12 ASN A 55 ASN A 62 -1 O CYS A 61 N THR A 6 SHEET 3 A12 GLU A 65 PRO A 76 -1 O GLU A 65 N ASN A 62 SHEET 4 A12 TRP A 84 THR A 93 -1 O GLU A 89 N GLN A 71 SHEET 5 A12 CYS A 119 ASP A 127 1 O GLN A 123 N ILE A 88 SHEET 6 A12 LYS B 143 HIS B 152 -1 O LEU B 149 N LEU A 124 SHEET 7 A12 LYS A 143 HIS A 152 -1 N GLY A 148 O HIS B 146 SHEET 8 A12 LEU B 121 ASP B 127 -1 O THR B 126 N GLU A 147 SHEET 9 A12 TRP B 84 THR B 93 1 N ILE B 88 O GLN B 123 SHEET 10 A12 GLU B 65 PRO B 76 -1 N THR B 75 O ARG B 85 SHEET 11 A12 ASN B 55 ASN B 62 -1 N ILE B 58 O LEU B 70 SHEET 12 A12 THR B 6 GLU B 9 -1 N THR B 6 O CYS B 61 CISPEP 1 LYS A 36 PRO A 37 0 -0.02 CISPEP 2 LYS B 36 PRO B 37 0 -0.22 CRYST1 72.311 80.683 55.099 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 0.013829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018149 0.00000