HEADER HYDROLASE 21-NOV-15 5EWT TITLE CRYSTAL STRUCTURE OF EXOIII ENDONUCLEASE FROM SULFOLOBUS ISLANDICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE III XTH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS REY15A; SOURCE 3 ORGANISM_TAXID: 930945; SOURCE 4 STRAIN: REY15A; SOURCE 5 GENE: SIRE_0100; SOURCE 6 EXPRESSION_SYSTEM: SULFOLOBUS ISLANDICUS REY15A; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 930945; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: REY15A; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSESD KEYWDS AP ENDONUCLEASE, DISULFIDE BOND, HYPERTHERMOPHILIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.YAN,Z.L.YUAN,L.C.GU,Y.L.SHEN REVDAT 2 18-OCT-17 5EWT 1 REMARK REVDAT 1 23-NOV-16 5EWT 0 JRNL AUTH Z.YAN,Z.L.YUAN,L.C.GU,Y.L.SHEN JRNL TITL CRYSTAL STRUCTURE OF EXOIII ENDONUCLEASE FROM SULFOLOBUS JRNL TITL 2 ISLANDICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10PRE_2124: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 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 39.5785 - 4.3353 0.99 2167 143 0.1543 0.1734 REMARK 3 2 4.3353 - 3.4417 1.00 2133 141 0.1497 0.1705 REMARK 3 3 3.4417 - 3.0068 1.00 2150 136 0.1626 0.2075 REMARK 3 4 3.0068 - 2.7320 1.00 2113 142 0.1729 0.2074 REMARK 3 5 2.7320 - 2.5362 1.00 2113 144 0.1790 0.1951 REMARK 3 6 2.5362 - 2.3867 1.00 2138 143 0.1716 0.2080 REMARK 3 7 2.3867 - 2.2672 1.00 2098 139 0.1762 0.2418 REMARK 3 8 2.2672 - 2.1685 1.00 2140 145 0.1746 0.1954 REMARK 3 9 2.1685 - 2.0850 1.00 2085 138 0.1785 0.2162 REMARK 3 10 2.0850 - 2.0131 1.00 2107 144 0.1854 0.2368 REMARK 3 11 2.0131 - 1.9501 1.00 2116 140 0.1885 0.2306 REMARK 3 12 1.9501 - 1.8944 1.00 2105 142 0.1912 0.1893 REMARK 3 13 1.8944 - 1.8445 1.00 2096 141 0.1989 0.2436 REMARK 3 14 1.8445 - 1.7995 1.00 2109 145 0.2194 0.2693 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 2116 REMARK 3 ANGLE : 0.753 2863 REMARK 3 CHIRALITY : 0.054 311 REMARK 3 PLANARITY : 0.004 369 REMARK 3 DIHEDRAL : 10.542 1284 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 5EWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-14 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 : SSRF REMARK 200 BEAMLINE : BL17U 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.310 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 59.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 9.0, 20% PEG 6000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 27.48550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.74275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.22825 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 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 O HOH A 513 O HOH A 553 1.97 REMARK 500 O HOH A 485 O HOH A 540 1.99 REMARK 500 O HOH A 521 O HOH A 537 2.04 REMARK 500 O HOH A 493 O HOH A 562 2.06 REMARK 500 O HOH A 323 O HOH A 529 2.06 REMARK 500 OE2 GLU A 205 O HOH A 301 2.07 REMARK 500 O HOH A 520 O HOH A 537 2.09 REMARK 500 O HOH A 424 O HOH A 536 2.10 REMARK 500 O HOH A 440 O HOH A 527 2.11 REMARK 500 O HOH A 315 O HOH A 321 2.14 REMARK 500 O HOH A 313 O HOH A 509 2.18 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 O HOH A 470 O HOH A 517 2565 1.82 REMARK 500 O HOH A 504 O HOH A 530 4554 2.13 REMARK 500 O HOH A 549 O HOH A 558 2565 2.19 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 ALA A 13 -126.33 55.18 REMARK 500 LYS A 37 -152.63 -120.21 REMARK 500 PRO A 159 3.22 -67.48 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 594 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 595 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 596 DISTANCE = 6.77 ANGSTROMS DBREF 5EWT A 1 247 UNP F0NG49 F0NG49_SULIR 1 247 SEQADV 5EWT ALA A 105 UNP F0NG49 TYR 105 ENGINEERED MUTATION SEQRES 1 A 247 MET LYS ILE VAL SER TRP ASN VAL ASN GLY ILE ARG ALA SEQRES 2 A 247 ALA LEU LYS LYS ASN LEU ILE ASP PHE ILE GLU ASN ASN SEQRES 3 A 247 MET PHE GLU VAL ILE MET PHE GLN GLU THR LYS GLY ASP SEQRES 4 A 247 ILE VAL PRO LEU ASP PHE ILE MET MET GLY TYR GLU VAL SEQRES 5 A 247 ILE SER PHE PRO ALA LYS ARG LYS GLY TYR SER GLY VAL SEQRES 6 A 247 MET THR LEU THR LYS ILE LYS PRO ILE ASN VAL ILE LYS SEQRES 7 A 247 GLY LEU GLN ILE LYS GLU PHE ASP ASP GLU GLY ARG THR SEQRES 8 A 247 VAL THR LEU GLU LEU LYS ASP PHE TYR VAL ILE ASN ALA SEQRES 9 A 247 ALA PHE PRO ARG ALA GLY ASP ASN LEU GLU ARG LEU ASP SEQRES 10 A 247 PHE LYS LEU LYS PHE ASN ASN GLU ILE GLU ASN PHE VAL SEQRES 11 A 247 LEU LYS LEU ARG ARG ALA LYS PRO VAL ILE LEU CYS GLY SEQRES 12 A 247 ASP PHE ASN ILE ALA HIS GLN ASN ILE ASP GLY ALA PHE SEQRES 13 A 247 SER ASP PRO THR ILE PRO GLY LEU THR PRO GLN GLU ARG SEQRES 14 A 247 SER TRP PHE SER HIS PHE LEU SER LEU GLY PHE ILE ASP SEQRES 15 A 247 THR PHE ARG TYR LEU HIS PRO ASN VAL ARG LYS TYR SER SEQRES 16 A 247 TRP TRP SER TYR MET GLY LYS ALA ARG GLU LYS ASN LEU SEQRES 17 A 247 GLY LEU ARG LEU ASP TYR CYS ILE VAL SER GLU GLU LEU SEQRES 18 A 247 LYS ASP ARG ILE LYS MET ALA ASP ILE LEU ILE ASP ILE SEQRES 19 A 247 GLN GLY SER ASP HIS ALA PRO ILE ILE LEU GLU LEU THR FORMUL 2 HOH *296(H2 O) HELIX 1 AA1 ARG A 12 ALA A 14 5 3 HELIX 2 AA2 LEU A 15 ASN A 25 1 11 HELIX 3 AA3 VAL A 41 MET A 47 1 7 HELIX 4 AA4 ILE A 82 ASP A 87 1 6 HELIX 5 AA5 ARG A 115 ARG A 135 1 21 HELIX 6 AA6 GLN A 150 GLY A 154 5 5 HELIX 7 AA7 THR A 165 LEU A 178 1 14 HELIX 8 AA8 THR A 183 HIS A 188 1 6 HELIX 9 AA9 GLU A 220 ASP A 223 5 4 SHEET 1 AA1 6 GLU A 51 PHE A 55 0 SHEET 2 AA1 6 VAL A 65 THR A 69 -1 O THR A 67 N ILE A 53 SHEET 3 AA1 6 VAL A 30 GLN A 34 -1 N PHE A 33 O MET A 66 SHEET 4 AA1 6 LYS A 2 ASN A 7 1 N VAL A 4 O MET A 32 SHEET 5 AA1 6 ILE A 242 LEU A 246 -1 O LEU A 244 N ILE A 3 SHEET 6 AA1 6 ILE A 225 ILE A 230 -1 N MET A 227 O GLU A 245 SHEET 1 AA2 6 ASN A 75 LYS A 78 0 SHEET 2 AA2 6 THR A 91 GLU A 95 -1 O GLU A 95 N ASN A 75 SHEET 3 AA2 6 TYR A 100 ALA A 105 -1 O ASN A 103 N VAL A 92 SHEET 4 AA2 6 VAL A 139 ASP A 144 1 O ILE A 140 N ILE A 102 SHEET 5 AA2 6 ASP A 213 SER A 218 -1 O ILE A 216 N LEU A 141 SHEET 6 AA2 6 PHE A 180 ASP A 182 -1 N ILE A 181 O VAL A 217 SSBOND 1 CYS A 142 CYS A 215 1555 1555 2.06 CRYST1 79.138 79.138 54.971 90.00 90.00 90.00 P 41 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 0.012636 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018191 0.00000