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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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