PDB Short entry for 3FHF HEADER DNA REPAIR, HYDROLASE, LYASE 09-DEC-08 3FHF TITLE CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII 8-OXOGUANINE DNA TITLE 2 GLYCOSYLASE (MJOGG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MJOGG; 8-OXOGUANINE DNA GLYCOSYLASE; DNA-(APURINIC OR COMPND 5 APYRIMIDINIC SITE) LYASE; AP LYASE; COMPND 6 EC: 3.2.2.-, 4.2.99.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: 1451601, MJ0724, OGG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS OGG, HELIX-HAIRPIN-HELIX, GLYCOSYLASE, 8-OXOGUANINE, 8-OXOG, MJOGG, KEYWDS 2 DNA DAMAGE, DNA REPAIR, GLYCOSIDASE, HYDROLASE, LYASE, KEYWDS 3 MULTIFUNCTIONAL ENZYME, NUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FAUCHER,S.DOUBLIE REVDAT 2 21-MAR-12 3FHF 1 JRNL VERSN REVDAT 1 19-MAY-09 3FHF 0 JRNL AUTH F.FAUCHER,S.DUCLOS,V.BANDARU,S.S.WALLACE,S.DOUBLIE JRNL TITL CRYSTAL STRUCTURES OF TWO ARCHAEAL 8-OXOGUANINE DNA JRNL TITL 2 GLYCOSYLASES PROVIDE STRUCTURAL INSIGHT INTO JRNL TITL 3 GUANINE/8-OXOGUANINE DISTINCTION. JRNL REF STRUCTURE V. 17 703 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19446526 JRNL DOI 10.1016/J.STR.2009.03.007 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2736238.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15220 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) : 0.202 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 759 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2310 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 116 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1815 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.22000 REMARK 3 B22 (A**2) : 4.18000 REMARK 3 B33 (A**2) : -0.96000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.39000 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) : 0.13 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.70 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) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.420 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 56.01 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 : LIGAND.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 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. THE FRIEDEL PAIRS WERE USED IN REMARK 3 PHASING. 2. BULK SOLVENT MODEL USED IN REFINEMENT. REMARK 4 REMARK 4 3FHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-08. REMARK 100 THE RCSB ID CODE IS RCSB050594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794, 0.9796, 0.97166 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : ADJUSTABLE FOCUS K-B PAIR SI REMARK 200 PLUS PT, RH COATINGS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28691 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.995 REMARK 200 RESOLUTION RANGE LOW (A) : 19.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 30%, 0.1M SODIUM CITRATE, 1% REMARK 280 B-MERCAPTOETHANOL, PH 5.9, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.92000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 333 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 246 LIES ON A SPECIAL POSITION. 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 OE1 GLU A 185 OE1 GLU A 185 2656 1.98 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 LYS A 165 -65.32 79.32 REMARK 500 LEU A 206 -123.28 -108.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FHG RELATED DB: PDB DBREF 3FHF A 1 207 UNP Q58134 OGG1_METJA 1 207 SEQADV 3FHF GLY A -6 UNP Q58134 EXPRESSION TAG SEQADV 3FHF ASN A -5 UNP Q58134 EXPRESSION TAG SEQADV 3FHF HIS A -4 UNP Q58134 EXPRESSION TAG SEQADV 3FHF HIS A -3 UNP Q58134 EXPRESSION TAG SEQADV 3FHF HIS A -2 UNP Q58134 EXPRESSION TAG SEQADV 3FHF HIS A -1 UNP Q58134 EXPRESSION TAG SEQADV 3FHF HIS A 0 UNP Q58134 EXPRESSION TAG SEQRES 1 A 214 GLY ASN HIS HIS HIS HIS HIS MSE MSE LEU ILE LYS LYS SEQRES 2 A 214 ILE GLU GLU LEU LYS ASN SER GLU ILE LYS ASP ILE ILE SEQRES 3 A 214 ASP LYS ARG ILE GLN GLU PHE LYS SER PHE LYS ASN LYS SEQRES 4 A 214 SER ASN GLU GLU TRP PHE LYS GLU LEU CYS PHE CYS ILE SEQRES 5 A 214 LEU THR ALA ASN PHE THR ALA GLU GLY GLY ILE ARG ILE SEQRES 6 A 214 GLN LYS GLU ILE GLY ASP GLY PHE LEU THR LEU PRO ARG SEQRES 7 A 214 GLU GLU LEU GLU GLU LYS LEU LYS ASN LEU GLY HIS ARG SEQRES 8 A 214 PHE TYR ARG LYS ARG ALA GLU TYR ILE VAL LEU ALA ARG SEQRES 9 A 214 ARG PHE LYS ASN ILE LYS ASP ILE VAL GLU SER PHE GLU SEQRES 10 A 214 ASN GLU LYS VAL ALA ARG GLU PHE LEU VAL ARG ASN ILE SEQRES 11 A 214 LYS GLY ILE GLY TYR LYS GLU ALA SER HIS PHE LEU ARG SEQRES 12 A 214 ASN VAL GLY TYR ASP ASP VAL ALA ILE ILE ASP ARG HIS SEQRES 13 A 214 ILE LEU ARG GLU LEU TYR GLU ASN ASN TYR ILE ASP GLU SEQRES 14 A 214 ILE PRO LYS THR LEU SER ARG ARG LYS TYR LEU GLU ILE SEQRES 15 A 214 GLU ASN ILE LEU ARG ASP ILE GLY GLU GLU VAL ASN LEU SEQRES 16 A 214 LYS LEU SER GLU LEU ASP LEU TYR ILE TRP TYR LEU ARG SEQRES 17 A 214 THR GLY LYS VAL LEU LYS MODRES 3FHF MSE A 1 MET SELENOMETHIONINE MODRES 3FHF MSE A 2 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 2 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *153(H2 O) HELIX 1 1 HIS A -3 ASN A 12 1 16 HELIX 2 2 GLU A 14 SER A 28 1 15 HELIX 3 3 PHE A 29 LYS A 32 5 4 HELIX 4 4 SER A 33 ALA A 48 1 16 HELIX 5 5 THR A 51 GLY A 63 1 13 HELIX 6 6 ASP A 64 LEU A 69 1 6 HELIX 7 7 PRO A 70 LEU A 81 1 12 HELIX 8 8 PHE A 85 ARG A 97 1 13 HELIX 9 9 ARG A 98 LYS A 100 5 3 HELIX 10 10 ASN A 101 PHE A 109 1 9 HELIX 11 11 ASN A 111 ILE A 123 1 13 HELIX 12 12 GLY A 127 VAL A 138 1 12 HELIX 13 13 ASP A 147 ASN A 157 1 11 HELIX 14 14 SER A 168 VAL A 186 1 19 HELIX 15 15 LYS A 189 GLY A 203 1 15 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N MSE A 2 1555 1555 1.33 LINK C MSE A 2 N LEU A 3 1555 1555 1.33 CRYST1 89.440 37.840 75.010 90.00 116.08 90.00 C 1 2 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 0.011181 0.000000 0.005473 0.00000 SCALE2 0.000000 0.026427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014843 0.00000