HEADER DNA BINDING PROTEIN 07-NOV-14 4RSF OBSLTE 15-JUN-16 4RSF 5K5A TITLE STRUCTURE OF PNOB8-LIKE PARB N-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARB DOMAIN PROTEIN NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 1-287); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS 98/2; SOURCE 3 ORGANISM_TAXID: 555311; SOURCE 4 GENE: SSOL_1539; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SPO0J-LIKE, DNA SEGREGATION/ASPA BINDING, ASPA, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER,J.LEE,N.B.CHINNAM,D.BARILLA REVDAT 2 15-JUN-16 4RSF 1 OBSLTE REVDAT 1 16-SEP-15 4RSF 0 JRNL AUTH M.A.SCHUMACHER,N.K.TONTHAT,J.LEE,F.A.RODRIGUEZ-CASTANEDA, JRNL AUTH 2 N.B.CHINNAM,A.K.KALLIOMAA-SANFORD,I.W.NG,M.T.BARGE,P.L.SHAW, JRNL AUTH 3 D.BARILLA JRNL TITL STRUCTURES OF ARCHAEAL DNA SEGREGATION MACHINERY REVEAL JRNL TITL 2 BACTERIAL AND EUKARYOTIC LINKAGES. JRNL REF SCIENCE V. 349 1120 2015 JRNL REFN ISSN 0036-8075 JRNL PMID 26339031 JRNL DOI 10.1126/SCIENCE.AAA9046 REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16850 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 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 3.0200 - 2.8400 1.00 2481 360 0.4030 0.3700 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 60.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 102.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : -7.65000 REMARK 3 B33 (A**2) : 8.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.78000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4RSF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-14. REMARK 100 THE RCSB ID CODE IS RCSB087738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.989, 0.980, 0.9375 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16864 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.840 REMARK 200 RESOLUTION RANGE LOW (A) : 58.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 (%): 55.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, 0.1 M CITRATE, PH 4.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 51.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 132 REMARK 465 SER A 133 REMARK 465 LYS A 134 REMARK 465 ILE A 135 REMARK 465 VAL A 136 REMARK 465 SER A 137 REMARK 465 HIS A 138 REMARK 465 ALA A 139 REMARK 465 THR A 140 REMARK 465 GLN A 141 REMARK 465 PHE A 142 REMARK 465 SER A 143 REMARK 465 ALA A 144 REMARK 465 THR A 145 REMARK 465 GLU A 146 REMARK 465 SER A 147 REMARK 465 LYS A 148 REMARK 465 TYR A 272 REMARK 465 THR A 273 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 ILE A 13 -7.33 -58.74 REMARK 500 LEU A 25 -71.48 -35.84 REMARK 500 ASN A 29 -148.91 -133.41 REMARK 500 SER A 43 -136.59 79.87 REMARK 500 ILE A 45 -56.71 -130.85 REMARK 500 SER A 185 -169.05 -66.34 REMARK 500 THR A 199 68.71 -152.72 REMARK 500 THR A 207 40.94 -85.98 REMARK 500 GLN A 209 -34.30 -38.84 REMARK 500 TYR A 222 -83.35 -59.60 REMARK 500 ARG A 224 -85.36 -52.86 REMARK 500 SER A 269 -91.35 -56.07 REMARK 500 GLU A 275 -70.14 -47.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RS7 RELATED DB: PDB REMARK 900 RELATED ID: 4RS8 RELATED DB: PDB REMARK 900 RELATED ID: 4RSB RELATED DB: PDB DBREF 4RSF A 1 286 UNP D0KSP7 D0KSP7_SULS9 1 287 SEQADV 4RSF ASP A 53 UNP D0KSP7 ASN 53 CONFLICT SEQADV 4RSF ASN A 105 UNP D0KSP7 ASP 105 CONFLICT SEQADV 4RSF A UNP D0KSP7 GLU 280 DELETION SEQADV 4RSF ALA A 287 UNP D0KSP7 EXPRESSION TAG SEQRES 1 A 287 MSE THR GLU LEU THR TYR THR GLU GLU VAL VAL SER ILE SEQRES 2 A 287 GLU LYS LEU LYS GLU ASP ASP GLU PHE LYS THR LEU VAL SEQRES 3 A 287 PRO SER ASN ASN SER ARG GLU ASP LEU GLU LYS SER LEU SEQRES 4 A 287 ARG GLU LYS SER GLN ILE PHE PRO LEU ILE ALA ASP ARG SEQRES 5 A 287 ASP TYR VAL LEU ILE ASP GLY TYR THR ARG LEU ASP ILE SEQRES 6 A 287 MSE LYS LYS LEU GLY PHE LYS GLU VAL LYS ILE LEU LYS SEQRES 7 A 287 TYR ASP PHE ASP SER GLN GLN GLU ARG ASP LYS ALA TYR SEQRES 8 A 287 GLU LEU ILE TRP THR PHE ASN GLY VAL ARG ARG GLN LEU SEQRES 9 A 287 ASN LYS ASN GLU ARG LEU ALA LEU PHE GLN LYS ILE ALA SEQRES 10 A 287 ASP ARG ILE ALA LYS ILE GLN ALA SER LYS ASN LYS THR SEQRES 11 A 287 GLU GLU SER LYS ILE VAL SER HIS ALA THR GLN PHE SER SEQRES 12 A 287 ALA THR GLU SER LYS GLN ILE GLU GLU ASN GLU GLU PHE SEQRES 13 A 287 VAL THR LEU ASP ASP GLY THR THR ILE SER ALA LEU GLU SEQRES 14 A 287 TYR GLU ARG ILE LEU LYS GLU LEU ASP LYS GLU ASN LYS SEQRES 15 A 287 ALA LEU SER GLU SER ASP LYS ARG LYS MSE ALA ILE LEU SEQRES 16 A 287 ARG ILE ASN THR PRO TRP LEU LEU LYS TYR VAL THR ASP SEQRES 17 A 287 GLN LYS TYR LYS VAL PRO LEU ASP GLN ALA PHE ARG ILE SEQRES 18 A 287 TYR THR ARG VAL LYS ASP LEU GLY ILE LEU ASP LYS LEU SEQRES 19 A 287 LYS ASP LEU ALA PRO ALA LEU ARG ASP PRO LEU ILE THR SEQRES 20 A 287 THR ARG GLU GLY ARG LYS ILE ILE LEU ASN ASP GLU TYR SEQRES 21 A 287 ARG ASP LEU LEU GLU LYS ILE ILE SER LYS GLN TYR THR SEQRES 22 A 287 THR GLU ARG ALA ILE SER VAL LYS GLN LYS GLU ALA LEU SEQRES 23 A 287 ALA MODRES 4RSF MSE A 1 MET SELENOMETHIONINE MODRES 4RSF MSE A 66 MET SELENOMETHIONINE MODRES 4RSF MSE A 192 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 66 8 HET MSE A 192 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) HELIX 1 1 ASP A 19 VAL A 26 1 8 HELIX 2 2 ASN A 30 LEU A 35 1 6 HELIX 3 3 LEU A 35 ARG A 40 1 6 HELIX 4 4 GLY A 59 LYS A 67 1 9 HELIX 5 5 GLU A 86 VAL A 100 1 15 HELIX 6 6 ASN A 105 GLU A 131 1 27 HELIX 7 7 ILE A 150 GLU A 155 1 6 HELIX 8 8 ALA A 167 ASP A 178 1 12 HELIX 9 9 GLU A 186 THR A 199 1 14 HELIX 10 10 THR A 199 LYS A 204 1 6 HELIX 11 11 PRO A 214 LEU A 228 1 15 HELIX 12 12 ILE A 230 ASP A 236 1 7 HELIX 13 13 ALA A 238 THR A 248 1 11 HELIX 14 14 THR A 248 ASN A 257 1 10 HELIX 15 15 TYR A 260 SER A 269 1 10 HELIX 16 16 GLU A 275 LYS A 283 1 9 SHEET 1 A 4 TYR A 6 SER A 12 0 SHEET 2 A 4 GLU A 73 TYR A 79 -1 O LYS A 78 N THR A 7 SHEET 3 A 4 LEU A 48 ALA A 50 1 N LEU A 48 O LYS A 75 SHEET 4 A 4 LEU A 56 ASP A 58 -1 O ILE A 57 N ILE A 49 SHEET 1 B 2 PHE A 156 THR A 158 0 SHEET 2 B 2 THR A 164 SER A 166 -1 O ILE A 165 N VAL A 157 LINK C MSE A 1 N THR A 2 1555 1555 1.33 LINK C ILE A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N LYS A 67 1555 1555 1.33 LINK C LYS A 191 N MSE A 192 1555 1555 1.33 LINK C MSE A 192 N ALA A 193 1555 1555 1.33 CRYST1 102.400 62.000 62.000 90.00 109.70 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 0.009766 0.000000 0.003497 0.00000 SCALE2 0.000000 0.016129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017132 0.00000 HETATM 1 N MSE A 1 18.243 -9.028 -0.583 1.00141.13 N HETATM 2 CA MSE A 1 19.424 -9.309 -1.390 1.00127.95 C HETATM 3 C MSE A 1 19.242 -10.548 -2.261 1.00122.95 C HETATM 4 O MSE A 1 19.611 -11.649 -1.864 1.00106.56 O HETATM 5 CB MSE A 1 20.644 -9.482 -0.483 1.00104.50 C HETATM 6 CG MSE A 1 21.946 -9.760 -1.218 1.00136.16 C HETATM 7 SE MSE A 1 22.596 -8.232 -2.240 1.00192.97 SE HETATM 8 CE MSE A 1 24.131 -9.082 -3.091 1.00105.68 C