HEADER HYDROLASE 12-FEB-09 3G91 TITLE 1.2 ANGSTROM STRUCTURE OF THE EXONUCLEASE III HOMOLOGUE MTH0212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MTH0212; COMPND 5 EC: 3.1.11.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: DELTA H (DSM 1053); SOURCE 5 GENE: MTH0212, MTH212, MTH_212; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21_UX; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET_B_001-MTH212 (K116A) KEYWDS DOUBLE-STRAND SPECIFIC 3'-5' EXONUCLEASE, AP ENDONUCLEASE, 2'- KEYWDS 2 DESOXYURIDINE ENDONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LAKOMEK,A.DICKMANNS,R.FICNER REVDAT 6 01-NOV-23 3G91 1 REMARK SEQADV LINK REVDAT 5 01-NOV-17 3G91 1 REMARK REVDAT 4 23-JUN-10 3G91 1 JRNL REVDAT 3 19-MAY-10 3G91 1 JRNL REVDAT 2 12-MAY-10 3G91 1 JRNL REVDAT 1 09-MAR-10 3G91 0 JRNL AUTH K.LAKOMEK,A.DICKMANNS,E.CIIRDAEVA,L.SCHOMACHER,R.FICNER JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF DNA URIDINE ENDONUCLEASE JRNL TITL 2 MTH212 BOUND TO DNA JRNL REF J.MOL.BIOL. V. 399 604 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20434457 JRNL DOI 10.1016/J.JMB.2010.04.044 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.GEORG,L.SCHOMACHER,J.P.J.CHONG,A.I.MAJERNIK,M.RAABE, REMARK 1 AUTH 2 H.URLAUB,S.MULLER,E.CIIRDAEVA,W.KRAMER,H.-J.FRITZ REMARK 1 TITL THE METHANOTHERMOBACTER THERMAUTOTROPHICUS EXOIII HOMOLOGUE REMARK 1 TITL 2 MTH212 IS A DNA URIDINE ENDONUCLEASE REMARK 1 REF NUCLEIC ACIDS RES. V. 34 5325 2006 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 17012282 REMARK 1 DOI 10.1093/NAR/GKL604 REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.122 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3686 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 73130 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.117 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3397 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 67188 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2168 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 433 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2606.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 29 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 24979 REMARK 3 NUMBER OF RESTRAINTS : 32073 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.384 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.080 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.088 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC FACTOR WAS USED IN REMARK 3 REFINEMENT REMARK 4 REMARK 4 3G91 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.13100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3FZI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 20% (V/V) MPD, REMARK 280 40MM MGAC, 50MM SODIUM CACODYLATE PH 6.0; PROTEIN SOLUTION: REMARK 280 180MM KCL, 10MM KH2PO4/K2HPO4 PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.05500 REMARK 290 SMTRY3 2 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 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 HIS A 262 REMARK 465 HIS A 263 REMARK 465 HIS A 264 REMARK 465 HIS A 265 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 OD2 ASP A 104 CG LEU A 258 1.61 REMARK 500 O LYS A 231 CG1 VAL A 234 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 O HOH A 7130 O HOH A 7217 1656 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 15 CD - NE - CZ ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 19 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 LEU A 50 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 LEU A 50 N - CA - CB ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 51 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 57 CD - NE - CZ ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 57 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 65 CD - NE - CZ ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 65 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 90 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 103 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 TYR A 129 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 138 CD - NE - CZ ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 140 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 VAL A 176 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 VAL A 176 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 194 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 PHE A 196 CZ - CE2 - CD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 TYR A 208 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 TYR A 208 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 211 CD - NE - CZ ANGL. DEV. = 15.2 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 215 CD - NE - CZ ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 215 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ASP A 242 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES 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 SER A 69 -143.24 54.81 REMARK 500 ASP A 103 -63.16 79.21 REMARK 500 ASP A 103 -60.59 76.86 REMARK 500 PHE A 173 27.59 -145.13 REMARK 500 ARG A 211 18.74 51.63 REMARK 500 ARG A 211 12.26 57.91 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 A3001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 38 OE1 REMARK 620 2 GLU A 38 OE2 7.9 REMARK 620 3 GLU A 38 OE2 48.2 41.0 REMARK 620 4 PO4 A2001 O2 85.6 91.7 131.9 REMARK 620 5 HOH A7020 O 92.1 86.9 78.6 93.1 REMARK 620 6 HOH A7054 O 177.4 174.5 134.5 91.9 88.8 REMARK 620 7 HOH A7110 O 86.4 90.6 93.9 95.6 171.0 93.1 REMARK 620 8 HOH A7183 O 97.7 91.2 50.6 175.3 83.5 84.9 87.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 3021 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 3022 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FZI RELATED DB: PDB REMARK 900 1.9 ANGSTROM STRUCTURE OF THE THERMOPHILIC EXONUCLEASE III REMARK 900 HOMOLOGUE MTH0212 REMARK 900 RELATED ID: 3G00 RELATED DB: PDB REMARK 900 MTH0212 IN COMPLEX WITH A 9BP BLUNT END DSDNA AT 1.7 ANGSTROM REMARK 900 RELATED ID: 3G0A RELATED DB: PDB REMARK 900 MTH0212 WITH TWO BOUND MANGANESE IONS REMARK 900 RELATED ID: 3G0R RELATED DB: PDB REMARK 900 COMPLEX OF MTH0212 AND AN 8BP DSDNA WITH DISTORTED ENDS REMARK 900 RELATED ID: 3G1K RELATED DB: PDB REMARK 900 MTH0212 (WT) CRYSTALLIZED IN A MONOCLINIC SPACE GROUP REMARK 900 RELATED ID: 3G2C RELATED DB: PDB REMARK 900 MTH0212 IN COMPLEX WITH A SHORT SSDNA (CGTA) REMARK 900 RELATED ID: 3G2D RELATED DB: PDB REMARK 900 COMPLEX OF MTH0212 AND A 4 BP DSDNA WITH 3'-OVERHANG REMARK 900 RELATED ID: 3G38 RELATED DB: PDB REMARK 900 THE CATALYTICALLY INACTIVE MUTANT MTH0212 (D151N) IN COMPLEX WITH REMARK 900 AN 8 BP DSDNA REMARK 900 RELATED ID: 3G3C RELATED DB: PDB REMARK 900 MTH0212 (WT) IN COMPLEX WITH A 6BP DSDNA CONTAINING A SINGLE ONE REMARK 900 NUCLEOTIDE LONG 3'-OVERHANG REMARK 900 RELATED ID: 3G3Y RELATED DB: PDB REMARK 900 MTH0212 IN COMPLEX WITH SSDNA IN SPACE GROUP P32 REMARK 900 RELATED ID: 3G4T RELATED DB: PDB REMARK 900 MTH0212 (WT) IN COMPLEX WITH A 7BP DSDNA REMARK 900 RELATED ID: 3G8V RELATED DB: PDB REMARK 900 THE RATIONALLY DESIGNED CATALYTICALLY INACTIVE MUTANT MTH0212(D151N) REMARK 900 RELATED ID: 3GA6 RELATED DB: PDB REMARK 900 MTH0212 IN COMPLEX WITH TWO DNA HELICES DBREF 3G91 A 1 257 UNP O26314 O26314_METTH 1 257 SEQADV 3G91 ALA A 2 UNP O26314 THR 2 ENGINEERED MUTATION SEQADV 3G91 ALA A 116 UNP O26314 LYS 116 ENGINEERED MUTATION SEQADV 3G91 LEU A 258 UNP O26314 EXPRESSION TAG SEQADV 3G91 GLU A 259 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 260 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 261 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 262 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 263 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 264 UNP O26314 EXPRESSION TAG SEQADV 3G91 HIS A 265 UNP O26314 EXPRESSION TAG SEQRES 1 A 265 MET ALA VAL LEU LYS ILE ILE SER TRP ASN VAL ASN GLY SEQRES 2 A 265 LEU ARG ALA VAL HIS ARG LYS GLY PHE LEU LYS TRP PHE SEQRES 3 A 265 MET GLU GLU LYS PRO ASP ILE LEU CYS LEU GLN GLU ILE SEQRES 4 A 265 LYS ALA ALA PRO GLU GLN LEU PRO ARG LYS LEU ARG HIS SEQRES 5 A 265 VAL GLU GLY TYR ARG SER PHE PHE THR PRO ALA GLU ARG SEQRES 6 A 265 LYS GLY TYR SER GLY VAL ALA MET TYR THR LYS VAL PRO SEQRES 7 A 265 PRO SER SER LEU ARG GLU GLY PHE GLY VAL GLU ARG PHE SEQRES 8 A 265 ASP THR GLU GLY ARG ILE GLN ILE ALA ASP PHE ASP ASP SEQRES 9 A 265 PHE LEU LEU TYR ASN ILE TYR PHE PRO ASN GLY ALA MET SEQRES 10 A 265 SER GLU GLU ARG LEU LYS TYR LYS LEU GLU PHE TYR ASP SEQRES 11 A 265 ALA PHE LEU GLU ASP VAL ASN ARG GLU ARG ASP SER GLY SEQRES 12 A 265 ARG ASN VAL ILE ILE CYS GLY ASP PHE ASN THR ALA HIS SEQRES 13 A 265 ARG GLU ILE ASP LEU ALA ARG PRO LYS GLU ASN SER ASN SEQRES 14 A 265 VAL SER GLY PHE LEU PRO VAL GLU ARG ALA TRP ILE ASP SEQRES 15 A 265 LYS PHE ILE GLU ASN GLY TYR VAL ASP THR PHE ARG MET SEQRES 16 A 265 PHE ASN SER ASP PRO GLY GLN TYR THR TRP TRP SER TYR SEQRES 17 A 265 ARG THR ARG ALA ARG GLU ARG ASN VAL GLY TRP ARG LEU SEQRES 18 A 265 ASP TYR PHE PHE VAL ASN GLU GLU PHE LYS GLY LYS VAL SEQRES 19 A 265 LYS ARG SER TRP ILE LEU SER ASP VAL MET GLY SER ASP SEQRES 20 A 265 HIS CYS PRO ILE GLY LEU GLU ILE GLU LEU LEU GLU HIS SEQRES 21 A 265 HIS HIS HIS HIS HIS HET PO4 A2001 5 HET MG A3001 1 HET GOL A3011 6 HET PEG A3021 7 HET PG4 A3022 13 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PO4 O4 P 3- FORMUL 3 MG MG 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 PEG C4 H10 O3 FORMUL 6 PG4 C8 H18 O5 FORMUL 7 HOH *433(H2 O) HELIX 1 1 GLY A 13 LYS A 20 1 8 HELIX 2 2 GLY A 21 LYS A 30 1 10 HELIX 3 3 ALA A 42 LEU A 46 5 5 HELIX 4 4 PRO A 47 HIS A 52 1 6 HELIX 5 5 VAL A 88 THR A 93 1 6 HELIX 6 6 SER A 118 SER A 142 1 25 HELIX 7 7 ARG A 157 LEU A 161 5 5 HELIX 8 8 PRO A 164 SER A 168 5 5 HELIX 9 9 LEU A 174 ASN A 187 1 14 HELIX 10 10 THR A 192 ASN A 197 1 6 HELIX 11 11 GLU A 229 GLY A 232 5 4 SHEET 1 A 6 ARG A 57 THR A 61 0 SHEET 2 A 6 VAL A 71 THR A 75 -1 O THR A 75 N ARG A 57 SHEET 3 A 6 ILE A 33 GLN A 37 -1 N LEU A 34 O TYR A 74 SHEET 4 A 6 VAL A 3 ASN A 10 1 N ILE A 7 O CYS A 35 SHEET 5 A 6 ILE A 251 GLU A 256 -1 O LEU A 253 N ILE A 6 SHEET 6 A 6 VAL A 234 ILE A 239 -1 N LYS A 235 O GLU A 254 SHEET 1 B 6 SER A 81 ARG A 83 0 SHEET 2 B 6 ILE A 97 ASP A 101 -1 O ILE A 99 N ARG A 83 SHEET 3 B 6 LEU A 106 TYR A 111 -1 O ASN A 109 N GLN A 98 SHEET 4 B 6 VAL A 146 ASP A 151 1 O ILE A 147 N TYR A 108 SHEET 5 B 6 ASP A 222 ASN A 227 -1 O PHE A 225 N ILE A 148 SHEET 6 B 6 TYR A 189 ASP A 191 -1 N VAL A 190 O VAL A 226 LINK OE1BGLU A 38 MG MG A3001 1555 1555 1.94 LINK OE2AGLU A 38 MG MG A3001 1555 1555 2.14 LINK OE2BGLU A 38 MG MG A3001 1555 1555 2.92 LINK O2 PO4 A2001 MG MG A3001 1555 1555 2.03 LINK MG MG A3001 O HOH A7020 1555 1555 2.15 LINK MG MG A3001 O HOH A7054 1555 1555 2.06 LINK MG MG A3001 O HOH A7110 1555 1555 2.03 LINK MG MG A3001 O HOH A7183 1555 1555 1.97 SITE 1 AC1 14 ASN A 10 GLU A 38 TYR A 111 ASN A 114 SITE 2 AC1 14 ASP A 151 ASN A 153 HIS A 248 MG A3001 SITE 3 AC1 14 HOH A7020 HOH A7054 HOH A7110 HOH A7214 SITE 4 AC1 14 HOH A7216 HOH A7257 SITE 1 AC2 6 GLU A 38 PO4 A2001 HOH A7020 HOH A7054 SITE 2 AC2 6 HOH A7110 HOH A7183 SITE 1 AC3 7 ARG A 48 ARG A 51 ARG A 140 ASP A 141 SITE 2 AC3 7 HOH A7018 HOH A7161 HOH A7320 SITE 1 AC4 8 ARG A 51 HIS A 52 TYR A 56 ARG A 57 SITE 2 AC4 8 SER A 58 PHE A 59 HOH A7071 HOH A7218 SITE 1 AC5 3 VAL A 3 ASP A 32 GLU A 254 CRYST1 44.330 72.110 46.330 90.00 117.96 90.00 P 1 21 1 2 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 0.022558 0.000000 0.011974 0.00000 SCALE2 0.000000 0.013868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024437 0.00000