HEADER DNA BINDING PROTEIN 04-SEP-04 1XD7 TITLE CRYSTAL STRUCTURE OF A PUTATIVE DNA BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: YWNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YWNA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, WINGED HELIX DNA KEYWDS 2 BINDING, HYPOTHETICAL PROTEIN, PSI, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, NYSGXRC, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.AGARWAL,S.SWAMINATHAN,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 8 14-FEB-24 1XD7 1 REMARK REVDAT 7 03-FEB-21 1XD7 1 AUTHOR REMARK SEQADV REVDAT 6 16-JAN-19 1XD7 1 TITLE REMARK REVDAT 5 13-JUL-11 1XD7 1 VERSN REVDAT 4 24-FEB-09 1XD7 1 VERSN REVDAT 3 25-JAN-05 1XD7 1 AUTHOR KEYWDS REMARK REVDAT 2 19-OCT-04 1XD7 1 SOURCE REVDAT 1 21-SEP-04 1XD7 0 JRNL AUTH R.AGARWAL,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE DNA BINDING PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 220851.760 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.2 REMARK 3 NUMBER OF REFLECTIONS : 5294 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) : 0.260 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 162 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.022 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 428 REMARK 3 BIN R VALUE (WORKING SET) : 0.3990 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 13 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.128 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 883 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.42000 REMARK 3 B22 (A**2) : 16.87000 REMARK 3 B33 (A**2) : -2.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.98000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.43 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 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) : 1.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.100 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 50.63 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ELECTRON DENSITY WAS ABSENT OR WEAK REMARK 3 FOR THE MISSING RESIDUES. DATA COLLECTED WITH NATIVE CRYSTAL WAS REMARK 3 USED FOR REFINEMENT. REMARK 4 REMARK 4 1XD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9793, 0.9400, 1.100 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CBASS REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5553 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 86.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 39.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 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, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULFATE, SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 32.94600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.68100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.94600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.68100 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 300 REMARK: THE SECOND PART OF THE DIMER IS GENERATED BY THE SYMMETRY REMARK 300 OPERATOR -X, Y, -Z 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: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 2 REMARK 465 LEU A 3 REMARK 465 ILE A 4 REMARK 465 ASN A 5 REMARK 465 GLN A 83 REMARK 465 GLU A 84 REMARK 465 GLU A 85 REMARK 465 LEU A 86 REMARK 465 PHE A 87 REMARK 465 ALA A 88 REMARK 465 VAL A 89 REMARK 465 HIS A 90 REMARK 465 GLU A 91 REMARK 465 ASN A 92 REMARK 465 PRO A 93 REMARK 465 HIS A 133 REMARK 465 LEU A 134 REMARK 465 PHE A 135 REMARK 465 GLU A 136 REMARK 465 GLY A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 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 ASP A 21 76.59 43.84 REMARK 500 ALA A 57 141.61 -23.27 REMARK 500 ALA A 62 -159.06 -150.55 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 SO4 A 190 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T1648 RELATED DB: TARGETDB DBREF 1XD7 A 4 135 UNP P71036 P71036_BACSU 2 133 SEQADV 1XD7 MET A 1 UNP P71036 CLONING ARTIFACT SEQADV 1XD7 SER A 2 UNP P71036 CLONING ARTIFACT SEQADV 1XD7 LEU A 3 UNP P71036 CLONING ARTIFACT SEQADV 1XD7 GLU A 136 UNP P71036 EXPRESSION TAG SEQADV 1XD7 GLY A 137 UNP P71036 EXPRESSION TAG SEQADV 1XD7 GLY A 138 UNP P71036 EXPRESSION TAG SEQADV 1XD7 SER A 139 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 140 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 141 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 142 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 143 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 144 UNP P71036 EXPRESSION TAG SEQADV 1XD7 HIS A 145 UNP P71036 EXPRESSION TAG SEQRES 1 A 145 MET SER LEU ILE ASN SER ARG LEU ALA VAL ALA ILE HIS SEQRES 2 A 145 ILE LEU SER LEU ILE SER MET ASP GLU LYS THR SER SER SEQRES 3 A 145 GLU ILE ILE ALA ASP SER VAL ASN THR ASN PRO VAL VAL SEQRES 4 A 145 VAL ARG ARG MET ILE SER LEU LEU LYS LYS ALA ASP ILE SEQRES 5 A 145 LEU THR SER ARG ALA GLY VAL PRO GLY ALA SER LEU LYS SEQRES 6 A 145 LYS ASP PRO ALA ASP ILE SER LEU LEU GLU VAL TYR ARG SEQRES 7 A 145 ALA VAL GLN LYS GLN GLU GLU LEU PHE ALA VAL HIS GLU SEQRES 8 A 145 ASN PRO ASN PRO LYS CYS PRO VAL GLY LYS LYS ILE GLN SEQRES 9 A 145 ASN ALA LEU ASP GLU THR PHE GLU SER VAL GLN ARG ALA SEQRES 10 A 145 MET GLU ASN GLU LEU ALA SER LYS SER LEU LYS ASP VAL SEQRES 11 A 145 MET ASN HIS LEU PHE GLU GLY GLY SER HIS HIS HIS HIS SEQRES 12 A 145 HIS HIS HET SO4 A 190 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *6(H2 O) HELIX 1 1 SER A 6 MET A 20 1 15 HELIX 2 2 SER A 25 ASN A 34 1 10 HELIX 3 3 ASN A 36 ALA A 50 1 15 HELIX 4 4 SER A 72 GLN A 81 1 10 HELIX 5 5 CYS A 97 ALA A 123 1 27 HELIX 6 6 SER A 126 MET A 131 1 6 SHEET 1 A 2 LEU A 53 THR A 54 0 SHEET 2 A 2 SER A 63 LEU A 64 -1 O SER A 63 N THR A 54 CISPEP 1 ASN A 94 PRO A 95 0 -0.22 SITE 1 AC1 8 SER A 25 SER A 26 ARG A 41 PRO A 60 SITE 2 AC1 8 GLY A 61 ARG A 116 ASN A 120 HOH A 196 CRYST1 65.892 49.362 51.510 90.00 121.61 90.00 C 1 2 1 4 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 0.015176 0.000000 0.009340 0.00000 SCALE2 0.000000 0.020258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022796 0.00000 CONECT 885 886 887 888 889 CONECT 886 885 CONECT 887 885 CONECT 888 885 CONECT 889 885 MASTER 290 0 1 6 2 0 2 6 894 1 5 12 END