HEADER HYDROLASE 23-MAY-16 5K5A TITLE STRUCTURE OF THE PNOB8-LIKE PARB N-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARB DOMAIN PROTEIN NUCLEASE; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 2-287; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 555311; SOURCE 4 STRAIN: 98/2; SOURCE 5 GENE: SSOL_1539; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PARB, PNOB8, PARTITION, DNA SEGREGATION, ARCHAEA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHUMACHER REVDAT 1 15-JUN-16 5K5A 0 SPRSDE 15-JUN-16 5K5A 4RSF 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 ESSN 1095-9203 JRNL PMID 26339031 JRNL DOI 10.1126/SCIENCE.AAA9046 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17036 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 883 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 58.3836 - 6.0850 0.99 1533 171 0.1941 0.1875 REMARK 3 2 6.0850 - 4.8306 0.97 1511 164 0.2426 0.3099 REMARK 3 3 4.8306 - 4.2202 1.00 1530 172 0.1880 0.2412 REMARK 3 4 4.2202 - 3.8344 1.00 1546 171 0.2198 0.3263 REMARK 3 5 3.8344 - 3.5596 1.00 1550 174 0.2466 0.2928 REMARK 3 6 3.5596 - 3.3498 1.00 1548 170 0.2786 0.3635 REMARK 3 7 3.3498 - 3.1820 1.00 1554 169 0.2797 0.3300 REMARK 3 8 3.1820 - 3.0435 1.00 1549 174 0.3298 0.4069 REMARK 3 9 3.0435 - 2.9264 1.00 1527 167 0.3487 0.3897 REMARK 3 10 2.9264 - 2.8254 0.97 1493 163 0.3733 0.3998 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 71.69 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07270 REMARK 3 B22 (A**2) : -8.55100 REMARK 3 B33 (A**2) : 8.62370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.44010 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 : 0.003 2265 REMARK 3 ANGLE : 0.532 3036 REMARK 3 CHIRALITY : 0.037 346 REMARK 3 PLANARITY : 0.002 386 REMARK 3 DIHEDRAL : 14.361 903 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 5K5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1 REMARK 200 MONOCHROMATOR : NULL 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 : 17036 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.825 REMARK 200 RESOLUTION RANGE LOW (A) : 58.371 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.83 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) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CITRATE, VAPOR DIFFUSION, REMARK 280 HANGING 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 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 APPLY THE FOLLOWING TO CHAINS: 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 SER B 47 REMARK 465 GLU B 136 REMARK 465 SER B 137 REMARK 465 LYS B 138 REMARK 465 ILE B 139 REMARK 465 VAL B 140 REMARK 465 SER B 141 REMARK 465 HIS B 142 REMARK 465 ALA B 143 REMARK 465 THR B 144 REMARK 465 GLN B 145 REMARK 465 PHE B 146 REMARK 465 SER B 147 REMARK 465 ALA B 148 REMARK 465 THR B 149 REMARK 465 GLU B 150 REMARK 465 SER B 151 REMARK 465 LYS B 152 REMARK 465 SER B 273 REMARK 465 LYS B 274 REMARK 465 GLN B 275 REMARK 465 TYR B 276 REMARK 465 ARG B 292 REMARK 465 GLY B 293 REMARK 465 GLY B 294 REMARK 465 LYS B 295 REMARK 465 VAL B 296 REMARK 465 LYS B 297 REMARK 465 LYS B 298 REMARK 465 SER B 299 REMARK 465 SER B 300 REMARK 465 LYS B 301 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 3 CB OG REMARK 470 HIS B 4 CB CG ND1 CD2 CE1 NE2 REMARK 470 THR B 277 N REMARK 470 LYS B 291 CG CD CE NZ 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 MSE B 5 89.06 -156.84 REMARK 500 ASN B 33 -147.03 -130.20 REMARK 500 ILE B 49 -57.77 -127.88 REMARK 500 SER B 189 -169.36 -71.16 REMARK 500 THR B 211 38.91 -87.58 REMARK 500 TYR B 226 -74.45 -60.92 REMARK 500 ARG B 228 -71.63 -59.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K5D RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN HAD DEGRADED WITHIN ITS C-TERMINAL DOMAIN DURING REMARK 999 CRYSTALLIZATION. DBREF 5K5A B 5 301 UNP D0KSP7 D0KSP7_SULS9 1 298 SEQADV 5K5A GLY B 2 UNP D0KSP7 EXPRESSION TAG SEQADV 5K5A SER B 3 UNP D0KSP7 EXPRESSION TAG SEQADV 5K5A HIS B 4 UNP D0KSP7 EXPRESSION TAG SEQADV 5K5A ASP B 57 UNP D0KSP7 ASN 53 CONFLICT SEQADV 5K5A ASN B 109 UNP D0KSP7 ASP 105 CONFLICT SEQADV 5K5A B UNP D0KSP7 GLU 280 DELETION SEQRES 1 B 300 GLY SER HIS MSE THR GLU LEU THR TYR THR GLU GLU VAL SEQRES 2 B 300 VAL SER ILE GLU LYS LEU LYS GLU ASP ASP GLU PHE LYS SEQRES 3 B 300 THR LEU VAL PRO SER ASN ASN SER ARG GLU ASP LEU GLU SEQRES 4 B 300 LYS SER LEU ARG GLU LYS SER GLN ILE PHE PRO LEU ILE SEQRES 5 B 300 ALA ASP ARG ASP TYR VAL LEU ILE ASP GLY TYR THR ARG SEQRES 6 B 300 LEU ASP ILE MSE LYS LYS LEU GLY PHE LYS GLU VAL LYS SEQRES 7 B 300 ILE LEU LYS TYR ASP PHE ASP SER GLN GLN GLU ARG ASP SEQRES 8 B 300 LYS ALA TYR GLU LEU ILE TRP THR PHE ASN GLY VAL ARG SEQRES 9 B 300 ARG GLN LEU ASN LYS ASN GLU ARG LEU ALA LEU PHE GLN SEQRES 10 B 300 LYS ILE ALA ASP ARG ILE ALA LYS ILE GLN ALA SER LYS SEQRES 11 B 300 ASN LYS THR GLU GLU SER LYS ILE VAL SER HIS ALA THR SEQRES 12 B 300 GLN PHE SER ALA THR GLU SER LYS GLN ILE GLU GLU ASN SEQRES 13 B 300 GLU GLU PHE VAL THR LEU ASP ASP GLY THR THR ILE SER SEQRES 14 B 300 ALA LEU GLU TYR GLU ARG ILE LEU LYS GLU LEU ASP LYS SEQRES 15 B 300 GLU ASN LYS ALA LEU SER GLU SER ASP LYS ARG LYS MSE SEQRES 16 B 300 ALA ILE LEU ARG ILE ASN THR PRO TRP LEU LEU LYS TYR SEQRES 17 B 300 VAL THR ASP GLN LYS TYR LYS VAL PRO LEU ASP GLN ALA SEQRES 18 B 300 PHE ARG ILE TYR THR ARG VAL LYS ASP LEU GLY ILE LEU SEQRES 19 B 300 ASP LYS LEU LYS ASP LEU ALA PRO ALA LEU ARG ASP PRO SEQRES 20 B 300 LEU ILE THR THR ARG GLU GLY ARG LYS ILE ILE LEU ASN SEQRES 21 B 300 ASP GLU TYR ARG ASP LEU LEU GLU LYS ILE ILE SER LYS SEQRES 22 B 300 GLN TYR THR THR GLU ARG ALA ILE SER VAL LYS GLN LYS SEQRES 23 B 300 GLU ALA LEU LYS ARG GLY GLY LYS VAL LYS LYS SER SER SEQRES 24 B 300 LYS MODRES 5K5A MSE B 5 MET MODIFIED RESIDUE MODRES 5K5A MSE B 70 MET MODIFIED RESIDUE MODRES 5K5A MSE B 196 MET MODIFIED RESIDUE HET MSE B 5 8 HET MSE B 70 8 HET MSE B 196 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) HELIX 1 AA1 ASP B 23 VAL B 30 1 8 HELIX 2 AA2 ASN B 34 LEU B 39 1 6 HELIX 3 AA3 LEU B 39 ARG B 44 1 6 HELIX 4 AA4 GLY B 63 LYS B 71 1 9 HELIX 5 AA5 GLU B 90 VAL B 104 1 15 HELIX 6 AA6 ASN B 109 GLU B 135 1 27 HELIX 7 AA7 ILE B 154 GLU B 159 1 6 HELIX 8 AA8 ALA B 171 ASP B 182 1 12 HELIX 9 AA9 SER B 189 THR B 203 1 15 HELIX 10 AB1 THR B 203 THR B 211 1 9 HELIX 11 AB2 PRO B 218 LEU B 232 1 15 HELIX 12 AB3 ILE B 234 ASP B 240 1 7 HELIX 13 AB4 ALA B 242 THR B 252 1 11 HELIX 14 AB5 THR B 252 ASN B 261 1 10 HELIX 15 AB6 TYR B 264 ILE B 272 1 9 HELIX 16 AB7 THR B 278 VAL B 284 1 7 SHEET 1 AA1 4 TYR B 10 SER B 16 0 SHEET 2 AA1 4 GLU B 77 TYR B 83 -1 O LYS B 82 N THR B 11 SHEET 3 AA1 4 LEU B 52 ALA B 54 1 N LEU B 52 O LYS B 79 SHEET 4 AA1 4 LEU B 60 ASP B 62 -1 O ILE B 61 N ILE B 53 SHEET 1 AA2 2 PHE B 160 THR B 162 0 SHEET 2 AA2 2 THR B 168 SER B 170 -1 O ILE B 169 N VAL B 161 LINK C HIS B 4 N MSE B 5 1555 1555 1.33 LINK C MSE B 5 N THR B 6 1555 1555 1.33 LINK C ILE B 69 N MSE B 70 1555 1555 1.33 LINK C MSE B 70 N LYS B 71 1555 1555 1.33 LINK C LYS B 195 N MSE B 196 1555 1555 1.33 LINK C MSE B 196 N ALA B 197 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