10 20 30 40 50 60 70 80 1WEF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 25-MAY-04 1WEF
TITLE CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI K20A MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: A/G-SPECIFIC ADENINE GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: ADENINE GLYCOSYLASE; COMPND 6 EC: 3.2.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.HITOMI,A.S.ARVAI,J.A.TAINER
REVDAT 3 24-FEB-09 1WEF 1 VERSN REVDAT 2 18-JAN-05 1WEF 1 JRNL REVDAT 1 21-SEP-04 1WEF 0
JRNL AUTH R.C.MANUEL,K.HITOMI,A.S.ARVAI,P.G.HOUSE,A.J.KURTZ, JRNL AUTH 2 M.L.DODSON,A.K.MCCULLOUGH,J.A.TAINER,R.S.LLOYD JRNL TITL REACTION INTERMEDIATES IN THE CATALYTIC MECHANISM JRNL TITL 2 OF ESCHERICHIA COLI MUTY DNA GLYCOSYLASE JRNL REF J.BIOL.CHEM. V. 279 46930 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15326180 JRNL DOI 10.1074/JBC.M403944200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 781977.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 18513 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) : 0.200 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 898 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2819 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : -0.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.06 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.76 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) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 48.11 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 : PAR.FS4 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 : TOP.FS4 REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WEF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023488.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI MIRROR + NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18513 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.420 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K
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 41.84800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.66250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.84800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.66250 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 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 ALA A 20 66.32 -106.07 REMARK 500 LEU A 137 74.80 -154.67 REMARK 500 LYS A 196 69.40 39.26 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1096 DISTANCE = 7.11 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 300
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WEG RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH DIFFERENT MUTATION K142A REMARK 900 RELATED ID: 1WEI RELATED DB: PDB REMARK 900 THE SAME PROTEIN, K20A MUTANT COMPLEXED TO ADENINE
DBREF 1WEF A 1 225 UNP P17802 MUTY_ECOLI 1 225
SEQADV 1WEF ALA A 20 UNP P17802 LYS 20 ENGINEERED
SEQRES 1 A 225 MET GLN ALA SER GLN PHE SER ALA GLN VAL LEU ASP TRP SEQRES 2 A 225 TYR ASP LYS TYR GLY ARG ALA THR LEU PRO TRP GLN ILE SEQRES 3 A 225 ASP LYS THR PRO TYR LYS VAL TRP LEU SER GLU VAL MET SEQRES 4 A 225 LEU GLN GLN THR GLN VAL ALA THR VAL ILE PRO TYR PHE SEQRES 5 A 225 GLU ARG PHE MET ALA ARG PHE PRO THR VAL THR ASP LEU SEQRES 6 A 225 ALA ASN ALA PRO LEU ASP GLU VAL LEU HIS LEU TRP THR SEQRES 7 A 225 GLY LEU GLY TYR TYR ALA ARG ALA ARG ASN LEU HIS LYS SEQRES 8 A 225 ALA ALA GLN GLN VAL ALA THR LEU HIS GLY GLY LYS PHE SEQRES 9 A 225 PRO GLU THR PHE GLU GLU VAL ALA ALA LEU PRO GLY VAL SEQRES 10 A 225 GLY ARG SER THR ALA GLY ALA ILE LEU SER LEU SER LEU SEQRES 11 A 225 GLY LYS HIS PHE PRO ILE LEU ASP GLY ASN VAL LYS ARG SEQRES 12 A 225 VAL LEU ALA ARG CYS TYR ALA VAL SER GLY TRP PRO GLY SEQRES 13 A 225 LYS LYS GLU VAL GLU ASN LYS LEU TRP SER LEU SER GLU SEQRES 14 A 225 GLN VAL THR PRO ALA VAL GLY VAL GLU ARG PHE ASN GLN SEQRES 15 A 225 ALA MET MET ASP LEU GLY ALA MET ILE CYS THR ARG SER SEQRES 16 A 225 LYS PRO LYS CYS SER LEU CYS PRO LEU GLN ASN GLY CYS SEQRES 17 A 225 ILE ALA ALA ALA ASN ASN SER TRP ALA LEU TYR PRO GLY SEQRES 18 A 225 LYS LYS PRO LYS
HET SF4 A 300 8
HETNAM SF4 IRON/SULFUR CLUSTER
FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *164(H2 O)
HELIX 1 1 GLN A 2 GLY A 18 1 17 HELIX 2 2 LEU A 22 ILE A 26 5 5 HELIX 3 3 THR A 29 GLN A 41 1 13 HELIX 4 4 GLN A 44 PHE A 59 1 16 HELIX 5 5 THR A 61 ALA A 68 1 8 HELIX 6 6 PRO A 69 THR A 78 1 10 HELIX 7 7 TYR A 83 HIS A 100 1 18 HELIX 8 8 THR A 107 ALA A 113 1 7 HELIX 9 9 GLY A 118 GLY A 131 1 14 HELIX 10 10 ASP A 138 TYR A 149 1 12 HELIX 11 11 LYS A 157 THR A 172 1 16 HELIX 12 12 GLY A 176 ILE A 191 1 16 HELIX 13 13 LYS A 198 CYS A 202 5 5 HELIX 14 14 CYS A 208 ASN A 214 1 7 HELIX 15 15 SER A 215 TYR A 219 5 5
LINK FE2 SF4 A 300 SG CYS A 192 1555 1555 2.15 LINK FE3 SF4 A 300 SG CYS A 199 1555 1555 2.41 LINK FE1 SF4 A 300 SG CYS A 202 1555 1555 2.33 LINK FE4 SF4 A 300 SG CYS A 208 1555 1555 2.30
CISPEP 1 TYR A 219 PRO A 220 0 -0.27
SITE 1 AC1 7 CYS A 148 CYS A 192 CYS A 199 CYS A 202 SITE 2 AC1 7 GLN A 205 CYS A 208 ALA A 211
CRYST1 83.696 49.325 69.680 90.00 123.25 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 0.011948 0.000000 0.007833 0.00000
SCALE2 0.000000 0.020274 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017161 0.00000