PDB Short entry for 1R7J HEADER DNA BINDING PROTEIN 21-OCT-03 1R7J TITLE CRYSTAL STRUCTURE OF THE DNA-BINDING PROTEIN SSO10A FROM SULFOLOBUS TITLE 2 SOLFATARICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL PROTEIN SSO10A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 GENE: SSO10A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSSETABLUE(DE3)PLACI (NOVAGEN); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETBLUE-2 KEYWDS WINGED HELIX-TURN-HELIX, TWO-STRANDED ANTIPARALLEL COILED COIL, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST KEYWDS 3 COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.CHEN,L.R.CHEN,X.E.ZHOU,Y.WANG,M.A.KAHSAI,A.T.CLARK,S.P.EDMONDSON, AUTHOR 2 Z.-J.LIU,J.P.ROSE,B.C.WANG,J.W.SHRIVER,E.J.MEEHAN,SOUTHEAST AUTHOR 3 COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 5 14-FEB-24 1R7J 1 REMARK REVDAT 4 13-JUL-11 1R7J 1 VERSN REVDAT 3 24-FEB-09 1R7J 1 VERSN REVDAT 2 01-FEB-05 1R7J 1 AUTHOR KEYWDS REMARK REVDAT 1 20-JUL-04 1R7J 0 JRNL AUTH L.CHEN,L.R.CHEN,X.E.ZHOU,Y.WANG,M.A.KAHSAI,A.T.CLARK, JRNL AUTH 2 S.P.EDMONDSON,Z.J.LIU,J.P.ROSE,B.C.WANG,E.J.MEEHAN, JRNL AUTH 3 J.W.SHRIVER JRNL TITL THE HYPERTHERMOPHILE PROTEIN SSO10A IS A DIMER OF WINGED JRNL TITL 2 HELIX DNA-BINDING DOMAINS LINKED BY AN ANTIPARALLEL COILED JRNL TITL 3 COIL ROD. JRNL REF J.MOL.BIOL. V. 341 73 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15312764 JRNL DOI 10.1016/J.JMB.2004.05.044 REMARK 2 REMARK 2 RESOLUTION. 1.47 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 699335.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 20838 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) : 0.232 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1021 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2535 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 132 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 729 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : -5.18000 REMARK 3 B33 (A**2) : 3.64000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 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) : 1.220 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 56.72 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 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 18.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : 0.26400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SULFUR-SAS ON CR X-RAY REMARK 200 SOURCE REMARK 200 SOFTWARE USED: SOLVE, RESOLVE, ISAS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, POTASSIUM FLUORIDE, PH 7.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K 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 28.97000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.97000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.15000 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 57.94000 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 ALA A 1 REMARK 465 LYS A 2 REMARK 465 ILE A 93 REMARK 465 ARG A 94 REMARK 465 GLN A 95 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SSO-10A RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS INFORMED THAT THE DIFFERENCES BETWEEN REMARK 999 THEIR SEQUENCE AND THE DATABASE REFERENCE SEQUENCE REMARK 999 WERE DUE TO THEIR USING A SLIGHTLY DIFFERENT STRAIN REMARK 999 IN CLONING. DBREF 1R7J A 1 94 UNP Q5W1E8 Q5W1E8_SULSO 2 95 SEQADV 1R7J LYS A 4 UNP Q5W1E8 ARG 5 SEE REMARK 999 SEQADV 1R7J ARG A 51 UNP Q5W1E8 LYS 52 SEE REMARK 999 SEQADV 1R7J LYS A 72 UNP Q5W1E8 ARG 73 SEE REMARK 999 SEQADV 1R7J GLU A 75 UNP Q5W1E8 ASP 76 SEE REMARK 999 SEQADV 1R7J ARG A 94 UNP Q5W1E8 LYS 95 SEE REMARK 999 SEQADV 1R7J GLN A 95 UNP Q5W1E8 SEE REMARK 999 SEQRES 1 A 95 ALA LYS LYS LYS SER LYS LEU GLU ILE ILE GLN ALA ILE SEQRES 2 A 95 LEU GLU ALA CYS LYS SER GLY SER PRO LYS THR ARG ILE SEQRES 3 A 95 MET TYR GLY ALA ASN LEU SER TYR ALA LEU THR GLY ARG SEQRES 4 A 95 TYR ILE LYS MET LEU MET ASP LEU GLU ILE ILE ARG GLN SEQRES 5 A 95 GLU GLY LYS GLN TYR MET LEU THR LYS LYS GLY GLU GLU SEQRES 6 A 95 LEU LEU GLU ASP ILE ARG LYS PHE ASN GLU MET ARG LYS SEQRES 7 A 95 ASN MET ASP GLN LEU LYS GLU LYS ILE ASN SER VAL LEU SEQRES 8 A 95 SER ILE ARG GLN FORMUL 2 HOH *175(H2 O) HELIX 1 1 SER A 5 LYS A 18 1 14 HELIX 2 2 PRO A 22 ASN A 31 1 10 HELIX 3 3 SER A 33 LEU A 47 1 15 HELIX 4 4 THR A 60 SER A 92 1 33 SHEET 1 A 2 ILE A 50 GLU A 53 0 SHEET 2 A 2 GLN A 56 LEU A 59 -1 O MET A 58 N ARG A 51 CRYST1 57.940 72.300 30.290 90.00 90.00 90.00 P 21 21 2 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 0.017259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033014 0.00000