HEADER LYASE 28-MAY-14 4UNF TITLE CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS ENDONUCLEASE III-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE III-1; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.99.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS R1; SOURCE 3 ORGANISM_TAXID: 243230; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST14 KEYWDS LYASE, FES CLUSTER, BASE EXCISION REPAIR, DNA GLYCOSYLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SARRE,M.OKVIST,T.KLAR,D.HALL,A.O.SMALAS,S.MCSWEENEY,J.TIMMINS,E.MOE REVDAT 4 10-JAN-24 4UNF 1 REMARK LINK REVDAT 3 12-AUG-15 4UNF 1 JRNL REVDAT 2 29-JUL-15 4UNF 1 JRNL REVDAT 1 10-JUN-15 4UNF 0 JRNL AUTH A.SARRE,M.OKVIST,T.KLAR,D.R.HALL,A.O.SMALAS,S.MCSWEENEY, JRNL AUTH 2 J.TIMMINS,E.MOE JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF TWO UNUSUAL JRNL TITL 2 ENDONUCLEASE III ENZYMES FROM DEINOCOCCUS RADIODURANS. JRNL REF J.STRUCT.BIOL. V. 191 87 2015 JRNL REFN ISSN 1047-8477 JRNL PMID 26172070 JRNL DOI 10.1016/J.JSB.2015.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 710 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 34.1965 - 3.6753 1.00 2778 144 0.1353 0.1601 REMARK 3 2 3.6753 - 2.9177 1.00 2722 130 0.1492 0.2031 REMARK 3 3 2.9177 - 2.5490 1.00 2668 146 0.1630 0.2089 REMARK 3 4 2.5490 - 2.3160 1.00 2645 157 0.1723 0.2347 REMARK 3 5 2.3160 - 2.1500 1.00 2664 133 0.2205 0.2851 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.31 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 : 0.011 1993 REMARK 3 ANGLE : 1.090 2734 REMARK 3 CHIRALITY : 0.047 299 REMARK 3 PLANARITY : 0.006 357 REMARK 3 DIHEDRAL : 13.641 757 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 12 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 80.4304 -4.5156 8.3792 REMARK 3 T TENSOR REMARK 3 T11: 0.2712 T22: 0.3192 REMARK 3 T33: 0.3082 T12: 0.1064 REMARK 3 T13: -0.0153 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 6.1451 L22: 6.5992 REMARK 3 L33: 4.2795 L12: 2.4473 REMARK 3 L13: 0.2377 L23: -1.1336 REMARK 3 S TENSOR REMARK 3 S11: 0.0424 S12: -0.2402 S13: -0.4275 REMARK 3 S21: 0.2529 S22: 0.0640 S23: -0.6035 REMARK 3 S31: 0.3637 S32: 0.4653 S33: -0.1453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 39 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.1803 18.6919 7.8994 REMARK 3 T TENSOR REMARK 3 T11: 0.3685 T22: 0.2680 REMARK 3 T33: 0.4648 T12: -0.0003 REMARK 3 T13: 0.0426 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 4.1654 L22: 3.0888 REMARK 3 L33: 1.6313 L12: -1.5918 REMARK 3 L13: -1.3067 L23: 0.0170 REMARK 3 S TENSOR REMARK 3 S11: -0.2752 S12: -0.2945 S13: -0.1438 REMARK 3 S21: 0.0420 S22: 0.2906 S23: -0.3144 REMARK 3 S31: 0.1765 S32: 0.1303 S33: -0.0658 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 64 THROUGH 85 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.4573 28.9691 7.2798 REMARK 3 T TENSOR REMARK 3 T11: 0.3864 T22: 0.3990 REMARK 3 T33: 0.5486 T12: 0.0180 REMARK 3 T13: 0.0666 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 4.2471 L22: 5.8047 REMARK 3 L33: 3.5985 L12: -0.7365 REMARK 3 L13: -3.9119 L23: 0.6671 REMARK 3 S TENSOR REMARK 3 S11: 0.0301 S12: -0.1498 S13: 0.2078 REMARK 3 S21: 0.1474 S22: 0.2867 S23: 0.8172 REMARK 3 S31: -0.1573 S32: -0.1229 S33: -0.1702 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 86 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.6631 18.4076 10.4366 REMARK 3 T TENSOR REMARK 3 T11: 0.3406 T22: 0.4670 REMARK 3 T33: 0.5972 T12: 0.0063 REMARK 3 T13: 0.0246 T23: -0.0365 REMARK 3 L TENSOR REMARK 3 L11: 2.2794 L22: 6.1117 REMARK 3 L33: 1.6904 L12: -0.0594 REMARK 3 L13: -0.7934 L23: -1.4195 REMARK 3 S TENSOR REMARK 3 S11: -0.1539 S12: 0.1702 S13: -0.0471 REMARK 3 S21: 0.2714 S22: 0.2681 S23: 1.1395 REMARK 3 S31: -0.1182 S32: -0.2823 S33: -0.0927 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 147 THROUGH 247 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.3883 3.4366 4.6341 REMARK 3 T TENSOR REMARK 3 T11: 0.2011 T22: 0.1534 REMARK 3 T33: 0.1683 T12: -0.0008 REMARK 3 T13: -0.0178 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 3.1315 L22: 2.1205 REMARK 3 L33: 3.5275 L12: -0.7374 REMARK 3 L13: -1.7113 L23: 0.4943 REMARK 3 S TENSOR REMARK 3 S11: 0.1007 S12: 0.0494 S13: 0.0901 REMARK 3 S21: 0.0221 S22: 0.0219 S23: -0.0386 REMARK 3 S31: -0.2006 S32: 0.0272 S33: -0.1176 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 4UNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.73505 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14192 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 45.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2ABK REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SUCCINIC ACID PH7.0, 0.1 M HEPES REMARK 280 PH7.0, 1% W/V PEG-MME 2000 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 90.69000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.27900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 90.69000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.27900 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2120 LIES ON A SPECIAL POSITION. 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 -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 2 REMARK 465 LEU A 3 REMARK 465 PHE A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 LYS A 10 REMARK 465 GLY A 11 REMARK 465 GLU A 248 REMARK 465 LYS A 249 REMARK 465 PRO A 250 REMARK 465 VAL A 251 REMARK 465 LYS A 252 REMARK 465 GLY A 253 REMARK 465 GLU A 254 REMARK 465 LYS A 255 REMARK 465 PRO A 256 REMARK 465 ALA A 257 REMARK 465 LYS A 258 REMARK 465 GLY A 259 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 GLN A 60 CG CD OE1 NE2 REMARK 470 ASP A 129 CG OD1 OD2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 247 O HOH A 2129 1.62 REMARK 500 O HOH A 2033 O HOH A 2035 2.17 REMARK 500 OD1 ASP A 40 O HOH A 2022 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 123 O HOH A 2066 1556 2.03 REMARK 500 O HOH A 2011 O HOH A 2056 1545 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 79 -179.65 -67.26 REMARK 500 VAL A 216 -64.66 -127.02 REMARK 500 ASP A 241 2.33 -66.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1249 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 115 O REMARK 620 2 LYS A 116 O 83.3 REMARK 620 3 ALA A 118 O 106.8 75.9 REMARK 620 4 GLY A 120 O 170.1 88.3 76.0 REMARK 620 5 GLY A 121 O 94.9 111.8 157.8 83.3 REMARK 620 6 HOH A2067 O 87.4 165.4 96.2 101.9 80.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1250 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 140 O REMARK 620 2 LEU A 142 O 92.9 REMARK 620 3 VAL A 145 O 92.6 87.3 REMARK 620 4 HOH A2074 O 64.9 149.9 112.4 REMARK 620 5 HOH A2077 O 176.6 88.4 84.3 115.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1248 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 217 SG REMARK 620 2 SF4 A1248 S2 119.4 REMARK 620 3 SF4 A1248 S3 109.4 104.9 REMARK 620 4 SF4 A1248 S4 114.2 102.7 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1248 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 224 SG REMARK 620 2 SF4 A1248 S1 109.9 REMARK 620 3 SF4 A1248 S2 116.2 103.7 REMARK 620 4 SF4 A1248 S4 116.1 105.2 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1248 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 227 SG REMARK 620 2 SF4 A1248 S1 115.1 REMARK 620 3 SF4 A1248 S3 112.8 104.0 REMARK 620 4 SF4 A1248 S4 114.7 103.9 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1248 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 233 SG REMARK 620 2 SF4 A1248 S1 111.2 REMARK 620 3 SF4 A1248 S2 112.0 104.8 REMARK 620 4 SF4 A1248 S3 118.2 104.7 104.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1252 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UOB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS ENDONUCLEASE III-3 DBREF 4UNF A 2 259 UNP Q9RRQ0 Q9RRQ0_DEIRA 2 259 SEQADV 4UNF MET A -5 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A -4 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A -3 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A -2 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A -1 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A 0 UNP Q9RRQ0 EXPRESSION TAG SEQADV 4UNF HIS A 1 UNP Q9RRQ0 EXPRESSION TAG SEQRES 1 A 265 MET HIS HIS HIS HIS HIS HIS THR LEU PHE GLY ASP VAL SEQRES 2 A 265 SER GLY LYS GLY ALA PRO LEU ASN ALA ALA ARG PRO ALA SEQRES 3 A 265 GLU GLU ARG ALA ALA LEU LEU ALA TRP VAL LYS GLU ARG SEQRES 4 A 265 LEU HIS GLU GLU TYR GLY ASP GLN ASP PRO THR PRO ARG SEQRES 5 A 265 ARG ASP PRO MET HIS GLU LEU ILE SER THR ILE LEU SER SEQRES 6 A 265 GLN ARG THR THR HIS ALA ASP GLU GLU ALA ALA TYR GLN SEQRES 7 A 265 GLU LEU ARG THR LEU GLY ASP TRP ASP ALA ILE THR LEU SEQRES 8 A 265 ALA PRO THR ASP ALA VAL ALA HIS ALA ILE ARG ARG SER SEQRES 9 A 265 ASN TYR PRO GLU SER LYS ALA PRO ARG ILE GLN GLU THR SEQRES 10 A 265 LEU ARG ARG ILE LYS ALA ALA PRO GLY GLY TYR ASP LEU SEQRES 11 A 265 ASP PHE LEU ARG ASP LEU PRO VAL LYS ASP ALA LEU LYS SEQRES 12 A 265 TRP LEU THR ASP LEU PRO GLY VAL GLY VAL LYS THR ALA SEQRES 13 A 265 SER LEU VAL LEU LEU PHE ASN TYR ALA ARG PRO VAL PHE SEQRES 14 A 265 PRO VAL ASP THR HIS VAL HIS ARG VAL SER THR ARG VAL SEQRES 15 A 265 GLY VAL ILE PRO ARG MET GLY GLU GLN ALA ALA HIS ARG SEQRES 16 A 265 ALA LEU LEU ALA LEU LEU PRO PRO ASP PRO PRO TYR LEU SEQRES 17 A 265 TYR GLU LEU HIS ILE ASN PHE LEU SER HIS GLY ARG GLN SEQRES 18 A 265 VAL CYS THR TRP THR ARG PRO LYS CYS GLY LYS CYS ILE SEQRES 19 A 265 LEU ARG GLU ARG CYS ASP ALA TYR ALA LEU TYR GLY ASP SEQRES 20 A 265 LYS VAL PRO SER PHE SER GLU LYS PRO VAL LYS GLY GLU SEQRES 21 A 265 LYS PRO ALA LYS GLY HET SF4 A1248 8 HET MG A1249 1 HET MG A1250 1 HET ACT A1251 4 HET ACT A1252 4 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION FORMUL 2 SF4 FE4 S4 FORMUL 3 MG 2(MG 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 HOH *129(H2 O) HELIX 1 1 LEU A 14 ARG A 18 5 5 HELIX 2 2 PRO A 19 GLY A 39 1 21 HELIX 3 3 ASP A 48 GLN A 60 1 13 HELIX 4 4 THR A 63 THR A 76 1 14 HELIX 5 5 ASP A 79 ALA A 86 1 8 HELIX 6 6 PRO A 87 ILE A 95 1 9 HELIX 7 7 TYR A 100 ALA A 118 1 19 HELIX 8 8 LEU A 124 LEU A 130 5 7 HELIX 9 9 PRO A 131 ASP A 141 1 11 HELIX 10 10 GLY A 146 ALA A 159 1 14 HELIX 11 11 ASP A 166 GLY A 177 1 12 HELIX 12 12 GLY A 183 ALA A 193 1 11 HELIX 13 13 ASP A 198 VAL A 216 1 19 HELIX 14 14 LYS A 223 CYS A 227 5 5 HELIX 15 15 LEU A 229 ARG A 232 5 4 HELIX 16 16 CYS A 233 GLY A 240 1 8 HELIX 17 17 ASP A 241 VAL A 243 5 3 LINK O ILE A 115 MG MG A1249 1555 1555 2.45 LINK O LYS A 116 MG MG A1249 1555 1555 2.66 LINK O ALA A 118 MG MG A1249 1555 1555 2.28 LINK O GLY A 120 MG MG A1249 1555 1555 2.57 LINK O GLY A 121 MG MG A1249 1555 1555 2.35 LINK O THR A 140 MG MG A1250 1555 1555 2.05 LINK O LEU A 142 MG MG A1250 1555 1555 2.69 LINK O VAL A 145 MG MG A1250 1555 1555 2.58 LINK SG CYS A 217 FE1 SF4 A1248 1555 1555 2.42 LINK SG CYS A 224 FE3 SF4 A1248 1555 1555 2.47 LINK SG CYS A 227 FE2 SF4 A1248 1555 1555 2.36 LINK SG CYS A 233 FE4 SF4 A1248 1555 1555 2.42 LINK MG MG A1249 O HOH A2067 1555 1555 2.54 LINK MG MG A1250 O HOH A2074 1555 1555 2.96 LINK MG MG A1250 O HOH A2077 1555 1555 2.57 SITE 1 AC1 4 CYS A 217 CYS A 224 CYS A 227 CYS A 233 SITE 1 AC2 6 ILE A 115 LYS A 116 ALA A 118 GLY A 120 SITE 2 AC2 6 GLY A 121 HOH A2067 SITE 1 AC3 5 THR A 140 LEU A 142 VAL A 145 HOH A2074 SITE 2 AC3 5 HOH A2077 SITE 1 AC4 5 ASN A 15 ARG A 18 ARG A 232 CYS A 233 SITE 2 AC4 5 ASP A 234 SITE 1 AC5 3 HOH A2092 HOH A2094 HOH A2126 CRYST1 181.380 38.558 37.094 90.00 89.34 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 0.005513 0.000000 -0.000064 0.00000 SCALE2 0.000000 0.025935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026960 0.00000