HEADER TRANSCRIPTION 24-FEB-04 1SGM TITLE CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN YXAF COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YXAF; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YXAF, S14F, BSU39990; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,S.SWAMINATHAN,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 7 14-FEB-24 1SGM 1 REMARK REVDAT 6 03-FEB-21 1SGM 1 AUTHOR JRNL REVDAT 5 11-OCT-17 1SGM 1 REMARK REVDAT 4 24-FEB-09 1SGM 1 VERSN REVDAT 3 21-NOV-06 1SGM 1 JRNL REVDAT 2 25-JAN-05 1SGM 1 AUTHOR KEYWDS REMARK REVDAT 1 17-AUG-04 1SGM 0 JRNL AUTH J.SEETHARAMAN,D.KUMARAN,J.B.BONANNO,S.K.BURLEY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE HTH-TYPE TRANSCRIPTIONAL JRNL TITL 2 REGULATOR YXAF FROM BACILLUS SUBTILIS. JRNL REF PROTEINS V. 63 1087 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 16475182 JRNL DOI 10.1002/PROT.20924 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 262329.970 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 24172 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) : 0.233 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2421 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3376 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 387 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.94000 REMARK 3 B22 (A**2) : 8.11000 REMARK 3 B33 (A**2) : -6.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.040 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 61.00 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788, 0.9792, 0.930 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CBASS REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 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 (%) : 99.6 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 FOR SHELL : NULL 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 (%): 43.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, MPD, PEG 1500, AMMONIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 50.17800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.47800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.17800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.47800 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: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 THR A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 189 REMARK 465 LYS A 190 REMARK 465 GLY A 191 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 189 REMARK 465 LYS B 190 REMARK 465 GLY B 191 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 LYS A 40 26.16 31.23 REMARK 500 PHE A 46 70.51 -110.38 REMARK 500 PHE A 47 108.32 -21.58 REMARK 500 PRO A 48 -135.43 23.11 REMARK 500 ASN A 49 -60.53 67.04 REMARK 500 PRO A 105 -58.50 -21.73 REMARK 500 SER A 117 96.85 24.72 REMARK 500 PHE B 47 169.35 -43.10 REMARK 500 PRO B 48 66.12 -28.05 REMARK 500 ASN B 49 -21.59 -157.85 REMARK 500 ASP B 96 15.68 -68.17 REMARK 500 PRO B 105 -63.39 -25.54 REMARK 500 SER B 117 97.53 83.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T1414 RELATED DB: TARGETDB DBREF 1SGM A 1 191 UNP P42105 YXAF_BACSU 1 191 DBREF 1SGM B 1 191 UNP P42105 YXAF_BACSU 1 191 SEQRES 1 A 191 MET THR SER ARG GLY ASP SER ARG GLU LYS ILE LEU HIS SEQRES 2 A 191 THR ALA SER ARG LEU SER GLN LEU GLN GLY TYR HIS ALA SEQRES 3 A 191 THR GLY LEU ASN GLN ILE VAL LYS GLU SER GLY ALA PRO SEQRES 4 A 191 LYS GLY SER LEU TYR HIS PHE PHE PRO ASN GLY LYS GLU SEQRES 5 A 191 GLU LEU ALA ILE GLU ALA VAL THR TYR THR GLY LYS ILE SEQRES 6 A 191 VAL GLU HIS LEU ILE GLN GLN SER MET ASP GLU SER SER SEQRES 7 A 191 ASP PRO VAL GLU ALA ILE GLN LEU PHE ILE LYS LYS THR SEQRES 8 A 191 ALA SER GLN PHE ASP ASN THR GLU SER ILE LYS GLY ILE SEQRES 9 A 191 PRO VAL GLY LEU LEU ALA SER GLU THR ALA LEU ILE SER SEQRES 10 A 191 GLU PRO LEU ARG THR VAL CYS MET LYS VAL PHE LYS SER SEQRES 11 A 191 TRP GLU ALA VAL PHE ALA ARG LYS LEU MET GLU ASN GLY SEQRES 12 A 191 PHE ALA GLU GLU GLU ALA ASN GLN LEU GLY THR LEU ILE SEQRES 13 A 191 ASN SER MET ILE GLU GLY GLY ILE MET LEU SER LEU THR SEQRES 14 A 191 ASN LYS ASP LYS THR PRO LEU LEU LEU ILE ALA GLU GLN SEQRES 15 A 191 ILE PRO VAL LEU VAL ARG LYS LYS GLY SEQRES 1 B 191 MET THR SER ARG GLY ASP SER ARG GLU LYS ILE LEU HIS SEQRES 2 B 191 THR ALA SER ARG LEU SER GLN LEU GLN GLY TYR HIS ALA SEQRES 3 B 191 THR GLY LEU ASN GLN ILE VAL LYS GLU SER GLY ALA PRO SEQRES 4 B 191 LYS GLY SER LEU TYR HIS PHE PHE PRO ASN GLY LYS GLU SEQRES 5 B 191 GLU LEU ALA ILE GLU ALA VAL THR TYR THR GLY LYS ILE SEQRES 6 B 191 VAL GLU HIS LEU ILE GLN GLN SER MET ASP GLU SER SER SEQRES 7 B 191 ASP PRO VAL GLU ALA ILE GLN LEU PHE ILE LYS LYS THR SEQRES 8 B 191 ALA SER GLN PHE ASP ASN THR GLU SER ILE LYS GLY ILE SEQRES 9 B 191 PRO VAL GLY LEU LEU ALA SER GLU THR ALA LEU ILE SER SEQRES 10 B 191 GLU PRO LEU ARG THR VAL CYS MET LYS VAL PHE LYS SER SEQRES 11 B 191 TRP GLU ALA VAL PHE ALA ARG LYS LEU MET GLU ASN GLY SEQRES 12 B 191 PHE ALA GLU GLU GLU ALA ASN GLN LEU GLY THR LEU ILE SEQRES 13 B 191 ASN SER MET ILE GLU GLY GLY ILE MET LEU SER LEU THR SEQRES 14 B 191 ASN LYS ASP LYS THR PRO LEU LEU LEU ILE ALA GLU GLN SEQRES 15 B 191 ILE PRO VAL LEU VAL ARG LYS LYS GLY FORMUL 3 HOH *236(H2 O) HELIX 1 1 ASP A 6 GLY A 23 1 18 HELIX 2 2 GLY A 28 GLY A 37 1 10 HELIX 3 3 GLY A 41 PHE A 46 1 6 HELIX 4 4 GLY A 50 GLU A 76 1 27 HELIX 5 5 ASP A 79 GLN A 94 1 16 HELIX 6 6 PHE A 95 ASP A 96 5 2 HELIX 7 7 ASN A 97 ILE A 101 5 5 HELIX 8 8 VAL A 106 ALA A 114 1 9 HELIX 9 9 SER A 117 ASN A 142 1 26 HELIX 10 10 ALA A 145 LYS A 171 1 27 HELIX 11 11 LYS A 173 GLU A 181 1 9 HELIX 12 12 GLN A 182 VAL A 187 1 6 HELIX 13 13 GLY B 5 GLY B 23 1 19 HELIX 14 14 GLY B 28 GLY B 37 1 10 HELIX 15 15 LYS B 40 PHE B 46 1 7 HELIX 16 16 ASN B 49 GLU B 76 1 28 HELIX 17 17 ASP B 79 SER B 93 1 15 HELIX 18 18 ASN B 97 ILE B 101 5 5 HELIX 19 19 VAL B 106 ALA B 114 1 9 HELIX 20 20 SER B 117 GLU B 141 1 25 HELIX 21 21 ALA B 145 LYS B 171 1 27 HELIX 22 22 LYS B 173 GLU B 181 1 9 HELIX 23 23 GLN B 182 VAL B 187 1 6 CRYST1 100.356 38.956 95.705 90.00 101.26 90.00 C 1 2 1 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 0.009965 0.000000 0.001984 0.00000 SCALE2 0.000000 0.025670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010654 0.00000