HEADER HYDROLASE 30-JAN-09 3G1K TITLE MTH0212 (WT) CRYSTALLIZED IN A MONOCLINIC SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A, B; 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-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET_B_001-MTH212 (WT) KEYWDS MAGNESIUM-DEPENDENT DOUBLE-STRAND SPECIFIC 3'-5' EXONUCLEASE, AP KEYWDS 2 ENDONUCLEASE, 2'-DEOXYURIDINE ENDONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LAKOMEK,A.DICKMANNS,R.FICNER REVDAT 6 01-NOV-23 3G1K 1 REMARK SEQADV LINK REVDAT 5 01-NOV-17 3G1K 1 REMARK REVDAT 4 23-JUN-10 3G1K 1 JRNL REVDAT 3 19-MAY-10 3G1K 1 JRNL REVDAT 2 12-MAY-10 3G1K 1 JRNL REVDAT 1 09-MAR-10 3G1K 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. 3.10 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10010 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 + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 512 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 689 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4270 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.63000 REMARK 3 B22 (A**2) : -2.50000 REMARK 3 B33 (A**2) : 6.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.550 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.408 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.851 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.841 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4386 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5914 ; 1.139 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 6.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;37.952 ;22.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 760 ;19.433 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;19.949 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 590 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3436 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2544 ; 0.333 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4100 ; 0.635 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1842 ; 0.758 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1814 ; 1.318 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 257 1 REMARK 3 1 B 2 B 257 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 2135 ; 0.02 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 2135 ; 0.03 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3G1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8148 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10535 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14800 REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33200 REMARK 200 FOR SHELL : 4.000 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 (%): 47.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 10% PEG, 100MM SODIUM REMARK 280 CACODYLATE PH 6.5; PROTEIN SOLUTION: 1MM MGCL2, 50MM KCL, 10MM REMARK 280 KH2PO4/K2HPO4 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 40.17250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 LEU A 258 REMARK 465 GLU A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 REMARK 465 HIS A 264 REMARK 465 HIS A 265 REMARK 465 MET B 1 REMARK 465 LEU B 258 REMARK 465 GLU B 259 REMARK 465 HIS B 260 REMARK 465 HIS B 261 REMARK 465 HIS B 262 REMARK 465 HIS B 263 REMARK 465 HIS B 264 REMARK 465 HIS B 265 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 GLU A 38 60.52 62.06 REMARK 500 LYS A 40 -41.33 64.18 REMARK 500 HIS A 52 76.06 -118.81 REMARK 500 SER A 69 -131.06 55.78 REMARK 500 ASP A 103 -54.58 66.45 REMARK 500 MET A 117 -23.80 87.42 REMARK 500 PHE A 173 19.00 -143.20 REMARK 500 ASP A 191 95.24 -69.46 REMARK 500 LYS B 40 -41.49 65.87 REMARK 500 HIS B 52 77.51 -118.27 REMARK 500 SER B 69 -131.47 55.21 REMARK 500 ASP B 103 -54.65 66.86 REMARK 500 MET B 117 -24.23 86.77 REMARK 500 PHE B 173 18.91 -143.68 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 A 266 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 12 OD1 REMARK 620 2 GLU A 38 OE2 86.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 266 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 12 OD1 REMARK 620 2 GLU B 38 OE2 87.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 266 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: 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: 3G91 RELATED DB: PDB REMARK 900 1.2 ANGSTROM STRUCTURE OF THE EXONUCLEASE III HOMOLOGUE MTH0212 REMARK 900 RELATED ID: 3GA6 RELATED DB: PDB REMARK 900 MTH0212 IN COMPLEX WITH TWO DNA HELICES DBREF 3G1K A 1 257 UNP O26314 O26314_METTH 1 257 DBREF 3G1K B 1 257 UNP O26314 O26314_METTH 1 257 SEQADV 3G1K ALA A 2 UNP O26314 THR 2 ENGINEERED MUTATION SEQADV 3G1K LEU A 258 UNP O26314 EXPRESSION TAG SEQADV 3G1K GLU A 259 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 260 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 261 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 262 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 263 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 264 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS A 265 UNP O26314 EXPRESSION TAG SEQADV 3G1K ALA B 2 UNP O26314 THR 2 ENGINEERED MUTATION SEQADV 3G1K LEU B 258 UNP O26314 EXPRESSION TAG SEQADV 3G1K GLU B 259 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 260 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 261 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 262 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 263 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 264 UNP O26314 EXPRESSION TAG SEQADV 3G1K HIS B 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 LYS 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 SEQRES 1 B 265 MET ALA VAL LEU LYS ILE ILE SER TRP ASN VAL ASN GLY SEQRES 2 B 265 LEU ARG ALA VAL HIS ARG LYS GLY PHE LEU LYS TRP PHE SEQRES 3 B 265 MET GLU GLU LYS PRO ASP ILE LEU CYS LEU GLN GLU ILE SEQRES 4 B 265 LYS ALA ALA PRO GLU GLN LEU PRO ARG LYS LEU ARG HIS SEQRES 5 B 265 VAL GLU GLY TYR ARG SER PHE PHE THR PRO ALA GLU ARG SEQRES 6 B 265 LYS GLY TYR SER GLY VAL ALA MET TYR THR LYS VAL PRO SEQRES 7 B 265 PRO SER SER LEU ARG GLU GLY PHE GLY VAL GLU ARG PHE SEQRES 8 B 265 ASP THR GLU GLY ARG ILE GLN ILE ALA ASP PHE ASP ASP SEQRES 9 B 265 PHE LEU LEU TYR ASN ILE TYR PHE PRO ASN GLY LYS MET SEQRES 10 B 265 SER GLU GLU ARG LEU LYS TYR LYS LEU GLU PHE TYR ASP SEQRES 11 B 265 ALA PHE LEU GLU ASP VAL ASN ARG GLU ARG ASP SER GLY SEQRES 12 B 265 ARG ASN VAL ILE ILE CYS GLY ASP PHE ASN THR ALA HIS SEQRES 13 B 265 ARG GLU ILE ASP LEU ALA ARG PRO LYS GLU ASN SER ASN SEQRES 14 B 265 VAL SER GLY PHE LEU PRO VAL GLU ARG ALA TRP ILE ASP SEQRES 15 B 265 LYS PHE ILE GLU ASN GLY TYR VAL ASP THR PHE ARG MET SEQRES 16 B 265 PHE ASN SER ASP PRO GLY GLN TYR THR TRP TRP SER TYR SEQRES 17 B 265 ARG THR ARG ALA ARG GLU ARG ASN VAL GLY TRP ARG LEU SEQRES 18 B 265 ASP TYR PHE PHE VAL ASN GLU GLU PHE LYS GLY LYS VAL SEQRES 19 B 265 LYS ARG SER TRP ILE LEU SER ASP VAL MET GLY SER ASP SEQRES 20 B 265 HIS CYS PRO ILE GLY LEU GLU ILE GLU LEU LEU GLU HIS SEQRES 21 B 265 HIS HIS HIS HIS HIS HET MG A 266 1 HET MG B 266 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *4(H2 O) HELIX 1 1 GLY A 13 ARG A 19 1 7 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 LEU A 174 ASN A 187 1 14 HELIX 9 9 PHE A 193 PHE A 196 5 4 HELIX 10 10 SER A 207 ARG A 211 5 5 HELIX 11 11 GLU A 229 GLY A 232 5 4 HELIX 12 12 GLY B 13 ARG B 19 1 7 HELIX 13 13 GLY B 21 LYS B 30 1 10 HELIX 14 14 ALA B 42 LEU B 46 5 5 HELIX 15 15 PRO B 47 HIS B 52 1 6 HELIX 16 16 VAL B 88 THR B 93 1 6 HELIX 17 17 SER B 118 SER B 142 1 25 HELIX 18 18 ARG B 157 LEU B 161 5 5 HELIX 19 19 LEU B 174 ASN B 187 1 14 HELIX 20 20 PHE B 193 PHE B 196 5 4 HELIX 21 21 SER B 207 ARG B 211 5 5 HELIX 22 22 GLU B 229 GLY B 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 MET A 73 N PHE A 59 SHEET 3 A 6 ILE A 33 GLN A 37 -1 N LEU A 36 O ALA A 72 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 ARG A 236 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 SHEET 1 C 6 ARG B 57 THR B 61 0 SHEET 2 C 6 VAL B 71 THR B 75 -1 O MET B 73 N PHE B 59 SHEET 3 C 6 ILE B 33 GLN B 37 -1 N LEU B 36 O ALA B 72 SHEET 4 C 6 VAL B 3 ASN B 10 1 N ILE B 7 O CYS B 35 SHEET 5 C 6 ILE B 251 GLU B 256 -1 O LEU B 253 N ILE B 6 SHEET 6 C 6 VAL B 234 ILE B 239 -1 N LYS B 235 O GLU B 254 SHEET 1 D 6 SER B 81 ARG B 83 0 SHEET 2 D 6 ILE B 97 ASP B 101 -1 O ILE B 99 N ARG B 83 SHEET 3 D 6 LEU B 106 TYR B 111 -1 O ASN B 109 N GLN B 98 SHEET 4 D 6 VAL B 146 ASP B 151 1 O ILE B 147 N TYR B 108 SHEET 5 D 6 ASP B 222 ASN B 227 -1 O PHE B 225 N ILE B 148 SHEET 6 D 6 TYR B 189 ASP B 191 -1 N VAL B 190 O VAL B 226 LINK OD1 ASN A 12 MG MG A 266 1555 1555 2.27 LINK OE2 GLU A 38 MG MG A 266 1555 1555 2.06 LINK OD1 ASN B 12 MG MG B 266 1555 1555 2.16 LINK OE2 GLU B 38 MG MG B 266 1555 1555 2.11 SITE 1 AC1 4 ASN A 10 ASN A 12 GLU A 38 ASP A 247 SITE 1 AC2 3 ASN B 12 GLU B 38 ASP B 247 CRYST1 44.635 80.345 81.839 90.00 90.32 90.00 P 1 21 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 0.022404 0.000000 0.000125 0.00000 SCALE2 0.000000 0.012446 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012219 0.00000