HEADER DNA BINDING PROTEIN 23-JAN-24 8VS5 TITLE STRUCTURE OF CATALYTIC DOMAIN OF TELOMERE RESOLVASE, REST, FROM TITLE 2 BORRELIA GARINII COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERE RESOLVASE REST; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIELLA GARINII; SOURCE 3 ORGANISM_TAXID: 29519; SOURCE 4 GENE: BGAPBR_B0003; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TELOMERE RESOLVASE, DNA-BINDING, STRUCTURAL GENOMICS, CENTER FOR KEYWDS 2 STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES, CSBID, DNA BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SEMPER,A.SAVCHENKO,N.WATANABE,CENTER FOR STRUCTURAL BIOLOGY OF AUTHOR 2 INFECTIOUS DISEASES (CSBID) REVDAT 3 28-AUG-24 8VS5 1 JRNL REVDAT 2 21-AUG-24 8VS5 1 JRNL REVDAT 1 17-JUL-24 8VS5 0 JRNL AUTH C.SEMPER,N.WATANABE,E.KARIMULLINA,D.T.PATEL,R.DI LEO, JRNL AUTH 2 M.CASTELLANOS,D.H.PATEL,G.CHACONAS,A.SAVCHENKO JRNL TITL STRUCTURE ANALYSIS OF THE TELOMERE RESOLVASE FROM THE LYME JRNL TITL 2 DISEASE SPIROCHETE BORRELIA GARINII REVEALS FUNCTIONAL JRNL TITL 3 DIVERGENCE OF ITS C-TERMINAL DOMAIN. JRNL REF NUCLEIC ACIDS RES. V. 52 8431 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38979576 JRNL DOI 10.1093/NAR/GKAE580 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 18265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1809 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 27.8300 - 6.5500 1.00 1325 146 0.2106 0.2428 REMARK 3 2 6.5500 - 5.2100 1.00 1340 147 0.1956 0.2059 REMARK 3 3 5.2100 - 4.5500 1.00 1324 146 0.1224 0.1413 REMARK 3 4 4.5500 - 4.1400 1.00 1315 146 0.1187 0.1462 REMARK 3 5 4.1400 - 3.8400 1.00 1332 157 0.1268 0.1595 REMARK 3 6 3.8400 - 3.6200 1.00 1343 142 0.1437 0.1915 REMARK 3 7 3.6200 - 3.4400 1.00 1305 141 0.1578 0.2143 REMARK 3 8 3.4400 - 3.2900 1.00 1322 148 0.1819 0.2184 REMARK 3 9 3.2900 - 3.1600 1.00 1317 147 0.1855 0.2559 REMARK 3 10 3.1600 - 3.0500 1.00 1336 150 0.2154 0.2818 REMARK 3 11 3.0500 - 2.9600 0.96 1281 136 0.2302 0.2412 REMARK 3 12 2.9600 - 2.8700 0.84 1126 120 0.2410 0.2698 REMARK 3 13 2.8700 - 2.8000 0.59 790 83 0.2515 0.2853 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.10 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 : 0.008 1495 REMARK 3 ANGLE : 0.943 2014 REMARK 3 CHIRALITY : 0.051 222 REMARK 3 PLANARITY : 0.005 254 REMARK 3 DIHEDRAL : 14.309 194 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 25.4353 10.9410 40.7779 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.2296 REMARK 3 T33: 0.1730 T12: -0.0344 REMARK 3 T13: 0.0324 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.0878 L22: 4.6168 REMARK 3 L33: 3.0163 L12: -0.4096 REMARK 3 L13: -0.2492 L23: 1.6289 REMARK 3 S TENSOR REMARK 3 S11: -0.0899 S12: 0.3056 S13: -0.0438 REMARK 3 S21: -0.2834 S22: 0.1000 S23: -0.0964 REMARK 3 S31: -0.1647 S32: 0.0699 S33: 0.0298 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 8VS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-18 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18265 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.796 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 23.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, 0.1M TRIS-HCL REMARK 280 PH 8.5, 12% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 55.14100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.58600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.58600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.71150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.58600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.58600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.57050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.58600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.58600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 82.71150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.58600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.58600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.57050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.14100 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: 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 LYS A 224 REMARK 465 LYS A 225 REMARK 465 ARG A 226 REMARK 465 GLU A 227 REMARK 465 ASN A 228 REMARK 465 ASN A 260 REMARK 465 LEU A 261 REMARK 465 THR A 262 REMARK 465 LYS A 263 REMARK 465 GLU A 264 REMARK 465 LEU A 265 REMARK 465 ILE A 266 REMARK 465 SER A 267 REMARK 465 SER A 268 REMARK 465 ASN A 269 REMARK 465 LEU A 270 REMARK 465 SER A 271 REMARK 465 HIS A 324 REMARK 465 GLU A 325 REMARK 465 PRO A 326 REMARK 465 ASN A 327 REMARK 465 ASP A 328 REMARK 465 ILE A 329 REMARK 465 THR A 330 REMARK 465 THR A 331 REMARK 465 ALA A 332 REMARK 465 PHE A 333 REMARK 465 HIS A 334 REMARK 465 TYR A 335 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 ASN A 215 28.88 -147.29 REMARK 500 ILE A 285 -58.68 -125.92 REMARK 500 ASN A 311 9.80 83.07 REMARK 500 LEU A 322 -100.98 -92.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 448 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 450 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 8.58 ANGSTROMS DBREF 8VS5 A 164 364 UNP B8F151 B8F151_BORGR 164 364 SEQADV 8VS5 ASN A 163 UNP B8F151 EXPRESSION TAG SEQRES 1 A 202 ASN VAL LYS ILE ASN LEU ASN THR TYR ILE GLU ILE ILE SEQRES 2 A 202 LYS LEU LEU LEU ASN GLN ASN ARG ASP ILE ARG LEU LYS SEQRES 3 A 202 PHE TYR GLY VAL LEU MET ALA ILE GLY ARG ARG PRO VAL SEQRES 4 A 202 GLU VAL MET LYS LEU SER GLN PHE TYR ILE ALA ASP LYS SEQRES 5 A 202 ASN HIS ILE ARG MET GLU PHE ILE ALA LYS LYS ARG GLU SEQRES 6 A 202 ASN ASN ILE ILE ASN GLU VAL VAL PHE PRO VAL PHE ALA SEQRES 7 A 202 ASP PRO GLU LEU ILE ILE ASN SER ILE LYS GLU ILE ARG SEQRES 8 A 202 TYR MET GLU GLN THR GLU ASN LEU THR LYS GLU LEU ILE SEQRES 9 A 202 SER SER ASN LEU SER TYR SER TYR ASN ARG LEU PHE ARG SEQRES 10 A 202 GLN ILE PHE ASN ASN ILE PHE ALA PRO GLU GLU SER VAL SEQRES 11 A 202 TYR PHE CYS ARG ALA ILE TYR CYS LYS PHE SER TYR LEU SEQRES 12 A 202 ALA PHE ALA PRO LYS ASN MET GLU MET ASN TYR TRP ILE SEQRES 13 A 202 THR LYS VAL LEU GLY HIS GLU PRO ASN ASP ILE THR THR SEQRES 14 A 202 ALA PHE HIS TYR ASN ARG TYR VAL LEU ASP ASN LEU ASN SEQRES 15 A 202 ASP LYS ALA ASP ASN ASN LEU LEU LYS LEU LEU ASN GLN SEQRES 16 A 202 ARG ILE TYR THR TYR VAL ARG FORMUL 2 HOH *52(H2 O) HELIX 1 AA1 LEU A 168 GLN A 181 1 14 HELIX 2 AA2 ASP A 184 GLY A 197 1 14 HELIX 3 AA3 ARG A 199 LYS A 205 1 7 HELIX 4 AA4 ASP A 241 THR A 258 1 18 HELIX 5 AA5 SER A 273 ASN A 283 1 11 HELIX 6 AA6 GLU A 290 ALA A 308 1 19 HELIX 7 AA7 GLU A 313 LEU A 322 1 10 HELIX 8 AA8 ASP A 348 TYR A 362 1 15 SHEET 1 AA1 2 ILE A 166 ASN A 167 0 SHEET 2 AA1 2 VAL A 339 LEU A 340 1 O LEU A 340 N ILE A 166 SHEET 1 AA2 3 GLN A 208 ILE A 211 0 SHEET 2 AA2 3 HIS A 216 PHE A 221 -1 O ARG A 218 N TYR A 210 SHEET 3 AA2 3 ASN A 232 PRO A 237 -1 O VAL A 234 N MET A 219 CRYST1 85.172 85.172 110.282 90.00 90.00 90.00 P 43 21 2 8 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 0.011741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009068 0.00000