HEADER DNA BINDING PROTEIN 06-AUG-18 6AEP TITLE CRYSTAL STRUCTURE OF THE SSDNA-BINDING DOMAIN OF DNAT FROM SALMONELLA TITLE 2 ENTERICA SEROVAR TYPHIMURIUM LT2 AT 1.84 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIMOSOMAL PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PRIMOSOMAL PROTEIN I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM STR. LT2; SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: DNAT, STM4544; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PRIMOSOME, REPLICATION RESTART, DNAT, DNA BINDING, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.HUANG,C.Y.HUANG REVDAT 2 22-NOV-23 6AEP 1 REMARK REVDAT 1 07-AUG-19 6AEP 0 JRNL AUTH Y.H.HUANG,C.Y.HUANG JRNL TITL CRYSTAL STRUCTURE OF THE SSDNA-BINDING DOMAIN OF DNAT FROM JRNL TITL 2 SALMONELLA ENTERICA SEROVAR TYPHIMURIUM LT2 AT 1.84 ANGSTROM JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 15826 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.7398 - 3.3493 0.98 2630 158 0.1935 0.2286 REMARK 3 2 3.3493 - 2.6591 0.99 2572 124 0.2296 0.2483 REMARK 3 3 2.6591 - 2.3232 0.98 2526 133 0.2323 0.2508 REMARK 3 4 2.3232 - 2.1109 0.97 2483 132 0.2215 0.2653 REMARK 3 5 2.1109 - 1.9596 0.98 2469 123 0.2462 0.3208 REMARK 3 6 1.9596 - 1.8441 0.92 2340 136 0.2693 0.3496 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1258 REMARK 3 ANGLE : 0.789 1709 REMARK 3 CHIRALITY : 0.044 169 REMARK 3 PLANARITY : 0.006 223 REMARK 3 DIHEDRAL : 11.761 733 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15843 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 28.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28400 REMARK 200 R SYM FOR SHELL (I) : 0.21300 REMARK 200 FOR SHELL : 4.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4OU6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M MAGNESIUM SULFATE, 100 MM MES REMARK 280 SODIUM SALT PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 34.45100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.45100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.64100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.76300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.64100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.76300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.45100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.64100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.76300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.45100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.64100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.76300 REMARK 290 SMTRY3 8 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: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 ILE A 163 REMARK 465 ASN A 164 REMARK 465 SER A 165 REMARK 465 VAL A 166 REMARK 465 SER A 167 REMARK 465 GLU A 168 REMARK 465 PRO A 169 REMARK 465 ASP A 170 REMARK 465 ASN A 171 REMARK 465 HIS A 172 REMARK 465 ILE A 173 REMARK 465 PRO A 174 REMARK 465 PRO A 175 REMARK 465 GLY A 176 REMARK 465 PHE A 177 REMARK 465 ARG A 178 REMARK 465 GLY A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 GLY B 156 REMARK 465 GLY B 157 REMARK 465 MET B 158 REMARK 465 PRO B 159 REMARK 465 GLN B 160 REMARK 465 ARG B 161 REMARK 465 ASP B 162 REMARK 465 ILE B 163 REMARK 465 ASN B 164 REMARK 465 SER B 165 REMARK 465 VAL B 166 REMARK 465 SER B 167 REMARK 465 GLU B 168 REMARK 465 PRO B 169 REMARK 465 ASP B 170 REMARK 465 ASN B 171 REMARK 465 HIS B 172 REMARK 465 ILE B 173 REMARK 465 PRO B 174 REMARK 465 PRO B 175 REMARK 465 GLY B 176 REMARK 465 PHE B 177 REMARK 465 ARG B 178 REMARK 465 GLY B 179 REMARK 465 HIS B 180 REMARK 465 HIS B 181 REMARK 465 HIS B 182 REMARK 465 HIS B 183 REMARK 465 HIS B 184 REMARK 465 HIS B 185 DBREF 6AEP A 84 179 UNP P67524 DNAT_SALTY 84 179 DBREF 6AEP B 84 179 UNP P67524 DNAT_SALTY 84 179 SEQADV 6AEP HIS A 180 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS A 181 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS A 182 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS A 183 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS A 184 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS A 185 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 180 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 181 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 182 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 183 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 184 UNP P67524 EXPRESSION TAG SEQADV 6AEP HIS B 185 UNP P67524 EXPRESSION TAG SEQRES 1 A 102 ILE PRO CYS GLY LYS PHE ALA MET TYR PRO ALA TRP GLN SEQRES 2 A 102 PRO ASP ALA ASP PHE GLN ARG GLN ALA ALA LEU TRP GLY SEQRES 3 A 102 VAL ALA LEU ARG GLU PRO VAL THR ALA GLU GLU LEU ALA SEQRES 4 A 102 ALA PHE ILE ALA TYR TRP GLN ALA GLU GLY LYS VAL PHE SEQRES 5 A 102 HIS HIS ILE GLN TRP GLN GLN LYS LEU ALA ARG SER VAL SEQRES 6 A 102 GLN ILE SER ARG SER SER ASN GLY GLY MET PRO GLN ARG SEQRES 7 A 102 ASP ILE ASN SER VAL SER GLU PRO ASP ASN HIS ILE PRO SEQRES 8 A 102 PRO GLY PHE ARG GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 102 ILE PRO CYS GLY LYS PHE ALA MET TYR PRO ALA TRP GLN SEQRES 2 B 102 PRO ASP ALA ASP PHE GLN ARG GLN ALA ALA LEU TRP GLY SEQRES 3 B 102 VAL ALA LEU ARG GLU PRO VAL THR ALA GLU GLU LEU ALA SEQRES 4 B 102 ALA PHE ILE ALA TYR TRP GLN ALA GLU GLY LYS VAL PHE SEQRES 5 B 102 HIS HIS ILE GLN TRP GLN GLN LYS LEU ALA ARG SER VAL SEQRES 6 B 102 GLN ILE SER ARG SER SER ASN GLY GLY MET PRO GLN ARG SEQRES 7 B 102 ASP ILE ASN SER VAL SER GLU PRO ASP ASN HIS ILE PRO SEQRES 8 B 102 PRO GLY PHE ARG GLY HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *106(H2 O) HELIX 1 AA1 ASP A 100 TRP A 108 1 9 HELIX 2 AA2 THR A 117 GLY A 132 1 16 HELIX 3 AA3 HIS A 136 SER A 153 1 18 HELIX 4 AA4 SER A 154 GLY A 156 5 3 HELIX 5 AA5 ASP B 100 TRP B 108 1 9 HELIX 6 AA6 THR B 117 GLY B 132 1 16 HELIX 7 AA7 HIS B 137 SER B 154 1 18 SHEET 1 AA1 2 PHE A 89 ALA A 90 0 SHEET 2 AA1 2 VAL A 134 PHE A 135 -1 O PHE A 135 N PHE A 89 SHEET 1 AA2 2 LYS B 88 ALA B 90 0 SHEET 2 AA2 2 VAL B 134 HIS B 136 -1 O PHE B 135 N PHE B 89 SSBOND 1 CYS A 86 CYS B 86 1555 7454 2.05 CRYST1 57.282 93.526 68.902 90.00 90.00 90.00 C 2 2 21 16 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 0.017457 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014513 0.00000