HEADER HYDROLASE 27-DEC-06 2E6L TITLE STRUCTURE OF MOUSE WRN EXONUCLEASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: WERNER SYNDROME ATP-DEPENDENT HELICASE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WRN EXONUCLEASE DOMAIN, RESIDUES 31-238; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: WRN; 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: PET-28A KEYWDS ZN-PROTEIN COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHO,J.M.CHOI REVDAT 3 13-MAR-24 2E6L 1 REMARK LINK REVDAT 2 24-FEB-09 2E6L 1 VERSN REVDAT 1 16-JAN-07 2E6L 0 JRNL AUTH Y.CHO,J.M.CHOI JRNL TITL PROBING THE ROLES OF ACTIVE SITE RESIDUES IN 3'-5' JRNL TITL 2 EXONUCLEASE OF WERNER SYNDROME PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 67763.480 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 531 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1592 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1465 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.65000 REMARK 3 B22 (A**2) : -3.43000 REMARK 3 B33 (A**2) : 5.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.05 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.340 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 46.04 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000026289. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-05; 14-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 93.15; NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PAL/PLS REMARK 200 BEAMLINE : 4A; 4A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2835; 1.2831, 1.2825, 1.2699 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11712 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.07600 REMARK 200 FOR SHELL : 40.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K 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 27.52350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.12250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.57350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.12250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.52350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.57350 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 LYS A 31 REMARK 465 SER A 32 REMARK 465 VAL A 33 REMARK 465 LEU A 34 REMARK 465 GLU A 35 REMARK 465 ASP A 36 REMARK 465 ILE A 82 REMARK 465 TYR A 83 REMARK 465 LYS A 84 REMARK 465 ASP A 226 REMARK 465 THR A 227 REMARK 465 VAL A 228 REMARK 465 GLN A 229 REMARK 465 VAL A 230 REMARK 465 PHE A 231 REMARK 465 ALA A 232 REMARK 465 LEU A 233 REMARK 465 ASN A 234 REMARK 465 LYS A 235 REMARK 465 ALA A 236 REMARK 465 GLU A 237 REMARK 465 GLU A 238 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 76 OD2 REMARK 620 2 GLU A 78 OE2 82.5 REMARK 620 3 ASP A 210 OD1 103.2 125.0 REMARK 620 4 HOH A 544 O 104.5 117.0 114.2 REMARK 620 5 HOH A 586 O 163.8 96.8 90.5 61.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 76 OD1 REMARK 620 2 HOH A 544 O 93.7 REMARK 620 3 HOH A 549 O 83.9 80.2 REMARK 620 4 HOH A 592 O 155.8 65.5 80.6 REMARK 620 5 HOH A 606 O 90.7 93.1 171.0 102.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E6M RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN APO FORM DBREF 2E6L A 31 238 UNP O09053 WRN_MOUSE 31 238 SEQADV 2E6L SER A 101 UNP O09053 ASN 101 SEE REMARK 999 SEQRES 1 A 208 LYS SER VAL LEU GLU ASP ASN LEU PRO PHE LEU GLU PHE SEQRES 2 A 208 PRO GLY SER ILE VAL TYR SER TYR GLU ALA SER ASP CYS SEQRES 3 A 208 SER PHE LEU SER GLU ASP ILE SER MET ARG LEU SER ASP SEQRES 4 A 208 GLY ASP VAL VAL GLY PHE ASP MET GLU TRP PRO PRO ILE SEQRES 5 A 208 TYR LYS PRO GLY LYS ARG SER ARG VAL ALA VAL ILE GLN SEQRES 6 A 208 LEU CYS VAL SER GLU SER LYS CYS TYR LEU PHE HIS ILE SEQRES 7 A 208 SER SER MET SER VAL PHE PRO GLN GLY LEU LYS MET LEU SEQRES 8 A 208 LEU GLU ASN LYS SER ILE LYS LYS ALA GLY VAL GLY ILE SEQRES 9 A 208 GLU GLY ASP GLN TRP LYS LEU LEU ARG ASP PHE ASP VAL SEQRES 10 A 208 LYS LEU GLU SER PHE VAL GLU LEU THR ASP VAL ALA ASN SEQRES 11 A 208 GLU LYS LEU LYS CYS ALA GLU THR TRP SER LEU ASN GLY SEQRES 12 A 208 LEU VAL LYS HIS VAL LEU GLY LYS GLN LEU LEU LYS ASP SEQRES 13 A 208 LYS SER ILE ARG CYS SER ASN TRP SER ASN PHE PRO LEU SEQRES 14 A 208 THR GLU ASP GLN LYS LEU TYR ALA ALA THR ASP ALA TYR SEQRES 15 A 208 ALA GLY LEU ILE ILE TYR GLN LYS LEU GLY ASN LEU GLY SEQRES 16 A 208 ASP THR VAL GLN VAL PHE ALA LEU ASN LYS ALA GLU GLU HET SO4 A 503 5 HET ZN A 501 1 HET ZN A 502 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 2 SO4 O4 S 2- FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *150(H2 O) HELIX 1 1 GLU A 52 LEU A 67 1 16 HELIX 2 2 ILE A 108 MET A 111 5 4 HELIX 3 3 PRO A 115 ASN A 124 1 10 HELIX 4 4 GLY A 133 ASP A 146 1 14 HELIX 5 5 LEU A 155 LEU A 163 1 9 HELIX 6 6 SER A 170 GLY A 180 1 11 HELIX 7 7 ASP A 186 CYS A 191 1 6 HELIX 8 8 THR A 200 ASN A 223 1 24 SHEET 1 A 6 SER A 46 SER A 50 0 SHEET 2 A 6 LYS A 102 PHE A 106 1 O LEU A 105 N VAL A 48 SHEET 3 A 6 VAL A 93 SER A 99 -1 N LEU A 96 O TYR A 104 SHEET 4 A 6 VAL A 72 GLU A 78 -1 N ASP A 76 O GLN A 95 SHEET 5 A 6 LYS A 128 GLY A 131 1 O ALA A 130 N PHE A 75 SHEET 6 A 6 PHE A 152 GLU A 154 1 O VAL A 153 N LYS A 129 LINK OD2 ASP A 76 ZN ZN A 501 1555 1555 2.14 LINK OD1 ASP A 76 ZN ZN A 502 1555 1555 2.14 LINK OE2 GLU A 78 ZN ZN A 501 1555 1555 2.03 LINK OD1 ASP A 210 ZN ZN A 501 1555 1555 2.08 LINK ZN ZN A 501 O HOH A 544 1555 1555 2.35 LINK ZN ZN A 501 O HOH A 586 1555 1555 2.66 LINK ZN ZN A 502 O HOH A 544 1555 1555 2.33 LINK ZN ZN A 502 O HOH A 549 1555 1555 2.18 LINK ZN ZN A 502 O HOH A 592 1555 1555 2.39 LINK ZN ZN A 502 O HOH A 606 1555 1555 2.32 CISPEP 1 PHE A 197 PRO A 198 0 0.10 SITE 1 AC1 6 LYS A 119 SER A 170 LEU A 171 ASN A 172 SITE 2 AC1 6 LYS A 185 HOH A 607 SITE 1 AC2 5 ASP A 76 GLU A 78 ASP A 210 HOH A 544 SITE 2 AC2 5 HOH A 586 SITE 1 AC3 5 ASP A 76 HOH A 544 HOH A 549 HOH A 592 SITE 2 AC3 5 HOH A 606 CRYST1 55.047 59.147 60.245 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 0.018166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016599 0.00000