HEADER NUCLEASE 26-MAY-97 1AKO TITLE EXONUCLEASE III FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXONUCLEASE III; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.11.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 CELL_LINE: BL21; SOURCE 6 GENE: XTH; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS NUCLEASE, EXONUCLEASE, AP-ENDONUCLEASE, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR C.D.MOL,C.-F.KUO,M.M.THAYER,R.P.CUNNINGHAM,J.A.TAINER REVDAT 4 07-FEB-24 1AKO 1 REMARK REVDAT 3 13-JUL-11 1AKO 1 VERSN REVDAT 2 24-FEB-09 1AKO 1 VERSN REVDAT 1 20-AUG-97 1AKO 0 JRNL AUTH C.D.MOL,C.F.KUO,M.M.THAYER,R.P.CUNNINGHAM,J.A.TAINER JRNL TITL STRUCTURE AND FUNCTION OF THE MULTIFUNCTIONAL DNA-REPAIR JRNL TITL 2 ENZYME EXONUCLEASE III. JRNL REF NATURE V. 374 381 1995 JRNL REFN ISSN 0028-0836 JRNL PMID 7885481 JRNL DOI 10.1038/374381A0 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.9 REMARK 3 NUMBER OF REFLECTIONS : 27067 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2769 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2112 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 270 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2183 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.391 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.19 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.181 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) : 1.470 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.230 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 3.370 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.250 ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 AN OVERALL BULK SOLVENT CORRECTION WAS APPLIED USNG X-PLOR V3.8 REMARK 3 AND LOW RESOLUTION DATA INCLUDED TO 20 ANGSTROMS REMARK 3 REMARK 3 THE THREE RAMACHANDRAN OUTLIER RESIDUES (TYR 63, GLU 114, REMARK 3 AND SER 178) ALL RESIDE IN LOOPS ON THE DNA BINDING SURFACE REMARK 3 OF THE ENZYME AND MAY PLAY ROLES IN ENZYME FUNCTION. REMARK 4 REMARK 4 1AKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-92 REMARK 200 TEMPERATURE (KELVIN) : 292 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN V. 1.3 REMARK 200 DATA SCALING SOFTWARE : XENGEN V. 1.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.0 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 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PHASES, X-PLOR 3.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 4000, 1.0 M IMIDAZOLE/ MALATE, REMARK 280 PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.26667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.53333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.53333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.26667 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: 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 TYR A 63 -145.84 49.78 REMARK 500 GLU A 114 -71.57 65.56 REMARK 500 SER A 178 -45.50 139.85 REMARK 500 PHE A 179 34.28 -142.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MG1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: MG BINDING SITE. DBREF 1AKO A 1 268 UNP P09030 EX3_ECOLI 1 268 SEQRES 1 A 268 MET LYS PHE VAL SER PHE ASN ILE ASN GLY LEU ARG ALA SEQRES 2 A 268 ARG PRO HIS GLN LEU GLU ALA ILE VAL GLU LYS HIS GLN SEQRES 3 A 268 PRO ASP VAL ILE GLY LEU GLN GLU THR LYS VAL HIS ASP SEQRES 4 A 268 ASP MET PHE PRO LEU GLU GLU VAL ALA LYS LEU GLY TYR SEQRES 5 A 268 ASN VAL PHE TYR HIS GLY GLN LYS GLY HIS TYR GLY VAL SEQRES 6 A 268 ALA LEU LEU THR LYS GLU THR PRO ILE ALA VAL ARG ARG SEQRES 7 A 268 GLY PHE PRO GLY ASP ASP GLU GLU ALA GLN ARG ARG ILE SEQRES 8 A 268 ILE MET ALA GLU ILE PRO SER LEU LEU GLY ASN VAL THR SEQRES 9 A 268 VAL ILE ASN GLY TYR PHE PRO GLN GLY GLU SER ARG ASP SEQRES 10 A 268 HIS PRO ILE LYS PHE PRO ALA LYS ALA GLN PHE TYR GLN SEQRES 11 A 268 ASN LEU GLN ASN TYR LEU GLU THR GLU LEU LYS ARG ASP SEQRES 12 A 268 ASN PRO VAL LEU ILE MET GLY ASP MET ASN ILE SER PRO SEQRES 13 A 268 THR ASP LEU ASP ILE GLY ILE GLY GLU GLU ASN ARG LYS SEQRES 14 A 268 ARG TRP LEU ARG THR GLY LYS CYS SER PHE LEU PRO GLU SEQRES 15 A 268 GLU ARG GLU TRP MET ASP ARG LEU MET SER TRP GLY LEU SEQRES 16 A 268 VAL ASP THR PHE ARG HIS ALA ASN PRO GLN THR ALA ASP SEQRES 17 A 268 ARG PHE SER TRP PHE ASP TYR ARG SER LYS GLY PHE ASP SEQRES 18 A 268 ASP ASN ARG GLY LEU ARG ILE ASP LEU LEU LEU ALA SER SEQRES 19 A 268 GLN PRO LEU ALA GLU CYS CYS VAL GLU THR GLY ILE ASP SEQRES 20 A 268 TYR GLU ILE ARG SER MET GLU LYS PRO SER ASP HIS ALA SEQRES 21 A 268 PRO VAL TRP ALA THR PHE ARG ARG FORMUL 2 HOH *190(H2 O) HELIX 1 1 LEU A 11 ALA A 13 5 3 HELIX 2 2 PRO A 15 HIS A 25 1 11 HELIX 3 3 ASP A 39 MET A 41 5 3 HELIX 4 4 LEU A 44 LYS A 49 1 6 HELIX 5 5 GLU A 85 ARG A 89 1 5 HELIX 6 6 LYS A 121 GLU A 139 1 19 HELIX 7 7 ASP A 158 ASP A 160 5 3 HELIX 8 8 GLU A 165 THR A 174 1 10 HELIX 9 9 PRO A 181 GLY A 194 1 14 HELIX 10 10 THR A 198 ALA A 202 1 5 HELIX 11 11 GLY A 219 ASP A 222 1 4 HELIX 12 12 GLN A 235 CYS A 240 1 6 HELIX 13 13 TYR A 248 SER A 252 1 5 SHEET 1 A 6 ASN A 53 HIS A 57 0 SHEET 2 A 6 VAL A 65 THR A 69 -1 N THR A 69 O ASN A 53 SHEET 3 A 6 VAL A 29 GLN A 33 -1 N LEU A 32 O ALA A 66 SHEET 4 A 6 LYS A 2 ASN A 7 1 N VAL A 4 O VAL A 29 SHEET 5 A 6 VAL A 262 PHE A 266 -1 N ALA A 264 O PHE A 3 SHEET 6 A 6 CYS A 241 ILE A 246 -1 N GLY A 245 O TRP A 263 SHEET 1 B 6 ALA A 75 ARG A 78 0 SHEET 2 B 6 ILE A 91 SER A 98 -1 N GLU A 95 O ALA A 75 SHEET 3 B 6 GLY A 101 TYR A 109 -1 N ASN A 107 O ILE A 92 SHEET 4 B 6 VAL A 146 ASP A 151 1 N LEU A 147 O THR A 104 SHEET 5 B 6 ASP A 229 SER A 234 -1 N LEU A 232 O ILE A 148 SHEET 6 B 6 LEU A 195 ASP A 197 -1 N VAL A 196 O ALA A 233 SITE 1 MG1 1 GLU A 34 CRYST1 107.800 107.800 42.800 90.00 90.00 120.00 P 31 2 1 6 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 0.009276 0.005356 0.000000 0.00000 SCALE2 0.000000 0.010712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023364 0.00000