HEADER HYDROLASE 11-JAN-20 6LPM TITLE CRYSTAL STRUCTURE OF AP ENDONUCLEASE FROM DEINOCOCCUS RADIODURAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE III; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.11.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 ATCC: 13939; SOURCE 5 GENE: XTH, DXG80_11425; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS AP ENDONUCLEASE, BASE EXCISION REPAIR, DNA REPAIR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,Y.HE REVDAT 3 29-NOV-23 6LPM 1 REMARK REVDAT 2 11-NOV-20 6LPM 1 JRNL REVDAT 1 27-MAY-20 6LPM 0 JRNL AUTH Y.HE,Y.WANG,C.QIN,Y.XU,K.CHENG,H.XU,B.TIAN,Y.ZHAO,L.WANG, JRNL AUTH 2 Y.HUA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A UNIQUE AP JRNL TITL 2 ENDONUCLEASE FROM DEINOCOCCUS RADIODURANS . JRNL REF FRONT MICROBIOL V. 11 1178 2020 JRNL REFN ESSN 1664-302X JRNL PMID 33117296 JRNL DOI 10.3389/FMICB.2020.01178 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 40435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1980 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 3.6014 - 2.8593 1.00 2843 155 0.1657 0.1806 REMARK 3 2 2.8593 - 2.4981 0.99 2792 165 0.1776 0.1931 REMARK 3 3 2.4981 - 2.2698 1.00 2821 155 0.1827 0.2214 REMARK 3 4 2.2698 - 2.1071 0.95 2653 131 0.2195 0.2289 REMARK 3 5 2.1071 - 1.9829 0.99 2776 132 0.1993 0.1993 REMARK 3 6 1.9829 - 1.8836 0.86 2416 122 0.2484 0.2690 REMARK 3 7 1.8836 - 1.8016 0.99 2777 131 0.1866 0.2639 REMARK 3 8 1.8016 - 1.7323 1.00 2772 142 0.1781 0.2220 REMARK 3 9 1.7323 - 1.6725 1.00 2815 127 0.1752 0.2117 REMARK 3 10 1.6725 - 1.6202 1.00 2761 154 0.1788 0.2101 REMARK 3 11 1.6202 - 1.5739 1.00 2779 143 0.1876 0.2074 REMARK 3 12 1.5739 - 1.5325 1.00 2752 159 0.1995 0.2526 REMARK 3 13 1.5325 - 1.5000 0.91 2533 111 0.3689 0.4044 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.71 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 : 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 33 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2996 18.7467 12.1230 REMARK 3 T TENSOR REMARK 3 T11: 0.1135 T22: 0.0996 REMARK 3 T33: 0.1219 T12: -0.0060 REMARK 3 T13: 0.0099 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 0.7480 L22: 0.4861 REMARK 3 L33: 0.8219 L12: -0.0993 REMARK 3 L13: 0.0730 L23: -0.2211 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: 0.0016 S13: 0.0294 REMARK 3 S21: 0.0174 S22: 0.0025 S23: 0.0065 REMARK 3 S31: -0.0221 S32: 0.0051 S33: -0.0084 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 6LPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.495 REMARK 200 RESOLUTION RANGE LOW (A) : 29.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.094 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.45 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2J5C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, PEG 5000, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.71000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.14000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.14000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.71000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.43000 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: 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 GLN A 8 REMARK 465 VAL A 9 REMARK 465 PRO A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 ALA A 17 REMARK 465 LEU A 18 REMARK 465 TRP A 19 REMARK 465 SER A 20 REMARK 465 ALA A 21 REMARK 465 PRO A 22 REMARK 465 MET A 23 REMARK 465 SER A 24 REMARK 465 ALA A 25 REMARK 465 PRO A 26 REMARK 465 ALA A 27 REMARK 465 ALA A 28 REMARK 465 PRO A 29 REMARK 465 PRO A 30 REMARK 465 LEU A 31 REMARK 465 THR A 32 REMARK 465 SER A 282 REMARK 465 GLU A 283 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 ARG A 71 -43.15 68.73 REMARK 500 SER A 95 -140.96 51.61 REMARK 500 ASN A 189 51.15 -95.25 REMARK 500 SER A 269 -174.84 -172.06 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 543 DISTANCE = 5.86 ANGSTROMS DBREF1 6LPM A 1 283 UNP A0A5C1MPK7_DEIRD DBREF2 6LPM A A0A5C1MPK7 1 283 SEQRES 1 A 283 MET SER LEU LEU ALA PRO ALA GLN VAL PRO GLY SER GLN SEQRES 2 A 283 SER SER HIS ALA LEU TRP SER ALA PRO MET SER ALA PRO SEQRES 3 A 283 ALA ALA PRO PRO LEU THR GLY PRO LEU LYS VAL THR THR SEQRES 4 A 283 PHE ASN VAL ASN GLY LEU ARG SER ALA LEU ARG LYS GLY SEQRES 5 A 283 LEU ALA ASP TRP VAL GLU SER ASN GLN PRO ASP VAL LEU SEQRES 6 A 283 LEU LEU GLN GLU VAL ARG ALA GLU PRO MET PRO ASP ALA SEQRES 7 A 283 LEU PRO GLY TYR HIS SER ALA TRP PHE PRO ALA GLN LYS SEQRES 8 A 283 ALA GLY TYR SER GLY VAL ALA ILE LEU SER ARG LEU PRO SEQRES 9 A 283 LEU LYS ASP VAL ARG LEU GLY MET PRO HIS ASP GLU MET SEQRES 10 A 283 ASP ALA GLU GLY ARG VAL VAL SER ALA VAL VAL ALA GLY SEQRES 11 A 283 VAL ARG PHE VAL SER VAL TYR LEU PRO SER GLY SER SER SEQRES 12 A 283 GLY GLU ALA ARG GLN GLY PHE LYS ASP ARG VAL LEU ALA SEQRES 13 A 283 ASP TYR GLN ALA TRP VAL SER GLU LEU LEU ALA ALA GLY SEQRES 14 A 283 GLU PRO VAL VAL ILE GLY GLY ASP TYR ASN ILE ALA HIS SEQRES 15 A 283 ARG GLU ILE ASP LEU LYS ASN TRP ARG SER ASN GLN LYS SEQRES 16 A 283 ASN SER GLY PHE LEU PRO HIS GLU ARG THR TRP MET THR SEQRES 17 A 283 ALA HIS LEU ALA ALA GLY LEU VAL ASP CYS HIS ARG ASP SEQRES 18 A 283 CYS LEU GLY GLU GLU ALA GLU TYR THR TRP TRP SER ASN SEQRES 19 A 283 ARG ALA ASN ALA TYR ALA ASN ASN VAL GLY TRP ARG ILE SEQRES 20 A 283 ASP TYR LEU LEU SER ALA GLY VAL ARG VAL SER GLY VAL SEQRES 21 A 283 ARG SER ASP ARG SER VAL ARG LEU SER ASP HIS ALA PRO SEQRES 22 A 283 LEU THR GLY TRP VAL GLU LEU GLU SER GLU FORMUL 2 HOH *243(H2 O) HELIX 1 AA1 GLY A 44 GLY A 52 1 9 HELIX 2 AA2 GLY A 52 GLN A 61 1 10 HELIX 3 AA3 HIS A 114 GLU A 120 1 7 HELIX 4 AA4 GLY A 144 GLY A 169 1 26 HELIX 5 AA5 ARG A 183 LEU A 187 5 5 HELIX 6 AA6 ASN A 189 ASN A 193 5 5 HELIX 7 AA7 LEU A 200 ALA A 213 1 14 HELIX 8 AA8 CYS A 218 GLY A 224 1 7 SHEET 1 AA1 6 HIS A 83 PHE A 87 0 SHEET 2 AA1 6 VAL A 97 SER A 101 -1 O SER A 101 N HIS A 83 SHEET 3 AA1 6 VAL A 64 GLN A 68 -1 N LEU A 65 O LEU A 100 SHEET 4 AA1 6 LEU A 35 ASN A 41 1 N THR A 38 O LEU A 66 SHEET 5 AA1 6 LEU A 274 GLU A 279 -1 O VAL A 278 N LEU A 35 SHEET 6 AA1 6 ARG A 256 SER A 262 -1 N SER A 258 O TRP A 277 SHEET 1 AA2 6 LYS A 106 LEU A 110 0 SHEET 2 AA2 6 VAL A 123 VAL A 128 -1 O VAL A 127 N LYS A 106 SHEET 3 AA2 6 VAL A 131 TYR A 137 -1 O PHE A 133 N ALA A 126 SHEET 4 AA2 6 VAL A 172 ASP A 177 1 O GLY A 175 N VAL A 134 SHEET 5 AA2 6 ASP A 248 ALA A 253 -1 O LEU A 251 N ILE A 174 SHEET 6 AA2 6 VAL A 216 ASP A 217 -1 N VAL A 216 O SER A 252 SHEET 1 AA3 2 TRP A 231 TRP A 232 0 SHEET 2 AA3 2 GLY A 244 TRP A 245 -1 O TRP A 245 N TRP A 231 CISPEP 1 MET A 112 PRO A 113 0 4.66 CRYST1 57.420 58.860 74.280 90.00 90.00 90.00 P 21 21 21 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 0.017416 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013463 0.00000