10 20 30 40 50 60 70 80 1J3E - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER REPLICATION/DNA 24-JAN-03 1J3E
TITLE CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH TITLE 2 N6-METHYLADENINE- GUANINE MISMATCH DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SEQA PROTEIN; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: DNA BINDING DOMAIN; COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: SEQA; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1
KEYWDS PROTEIN-DNA COMPLEX, RECOGNITION OF HEMIMETHYLATED DNA, KEYWDS 2 MISMATCHED DNA, REPLICATION, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, KEYWDS 4 REPLICATION/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.FUJIKAWA,H.KURUMIZAKA,O.NUREKI,Y.TANAKA,M.YAMAZOE, AUTHOR 2 S.HIRAGA,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 3 INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 1J3E 1 VERSN REVDAT 1 18-MAY-04 1J3E 0
JRNL AUTH N.FUJIKAWA,H.KURUMIZAKA,O.NUREKI,Y.TANAKA, JRNL AUTH 2 M.YAMAZOE,S.HIRAGA,S.YOKOYAMA JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSES OF JRNL TITL 2 HEMIMETHYLATED DNA BINDING BY THE SEQA PROTEIN JRNL REF NUCLEIC ACIDS RES. V. 32 82 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 14704346 JRNL DOI 10.1093/NAR/GKH173
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 343 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3552 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 40 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 : 908 REMARK 3 NUCLEIC ACID ATOMS : 407 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.52 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.41 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1J3E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-03. REMARK 100 THE RCSB ID CODE IS RCSB005580.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-02 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9740 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED FIXED EXIT REMARK 200 DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 6126 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 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 (%): 43.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CA-ACETATE, NA-CACODYLATE, PEG8K, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.71600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.58800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.53050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.58800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.71600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.53050 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 SER A 13 158.22 -45.86 REMARK 500 ASP A 37 69.85 -151.33 REMARK 500 ALA A 38 -28.07 -39.41 REMARK 500 THR A 52 -25.85 -147.29 REMARK 500 MET A 102 26.58 -72.86 REMARK 500 GLN A 103 80.46 27.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG B 203 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IU3 RELATED DB: PDB REMARK 900 RELATED ID: TRT001000146.2 RELATED DB: TARGETDB
DBREF 1J3E A 6 116 UNP P36658 SEQA_ECOLI 71 181 DBREF 1J3E B 201 210 PDB 1J3E 1J3E 201 210 DBREF 1J3E C 211 220 PDB 1J3E 1J3E 211 220
SEQADV 1J3E PRO A 2 UNP P36658 CLONING ARTIFACT SEQADV 1J3E LEU A 3 UNP P36658 CLONING ARTIFACT SEQADV 1J3E GLY A 4 UNP P36658 CLONING ARTIFACT SEQADV 1J3E SER A 5 UNP P36658 CLONING ARTIFACT
SEQRES 1 B 10 DA DA DG DG 6MA DT DC DC DA DA SEQRES 1 C 10 DT DT DG DG DA DG DC DC DT DT SEQRES 1 A 115 PRO LEU GLY SER ALA MET ARG GLU LEU LEU LEU SER ASP SEQRES 2 A 115 GLU TYR ALA GLU GLN LYS ARG ALA VAL ASN ARG PHE MET SEQRES 3 A 115 LEU LEU LEU SER THR LEU TYR SER LEU ASP ALA GLN ALA SEQRES 4 A 115 PHE ALA GLU ALA THR GLU SER LEU HIS GLY ARG THR ARG SEQRES 5 A 115 VAL TYR PHE ALA ALA ASP GLU GLN THR LEU LEU LYS ASN SEQRES 6 A 115 GLY ASN GLN THR LYS PRO LYS HIS VAL PRO GLY THR PRO SEQRES 7 A 115 TYR TRP VAL ILE THR ASN THR ASN THR GLY ARG LYS CYS SEQRES 8 A 115 SER MET ILE GLU HIS ILE MET GLN SER MET GLN PHE PRO SEQRES 9 A 115 ALA GLU LEU ILE GLU LYS VAL CYS GLY THR ILE
MODRES 1J3E 6MA B 205 A
HET 6MA B 205 22
HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
FORMUL 1 6MA C11 H16 N5 O6 P FORMUL 4 HOH *84(H2 O)
HELIX 1 1 PRO A 2 SER A 13 1 12 HELIX 2 2 SER A 13 GLN A 19 1 7 HELIX 3 3 ARG A 21 ASP A 37 1 17 HELIX 4 4 ASP A 37 SER A 47 1 11 HELIX 5 5 GLU A 60 ASN A 66 1 7 HELIX 6 6 ASN A 87 MET A 102 1 16 HELIX 7 7 PRO A 105 GLY A 114 1 10
SHEET 1 A 3 PHE A 56 ALA A 57 0 SHEET 2 A 3 TRP A 81 VAL A 82 -1 O TRP A 81 N ALA A 57 SHEET 3 A 3 LYS A 73 HIS A 74 -1 N LYS A 73 O VAL A 82
SSBOND 1 CYS A 92 CYS A 113 1555 1555 2.95
LINK O3' DG B 204 P 6MA B 205 1555 1555 1.60 LINK O3' 6MA B 205 P DT B 206 1555 1555 1.60
CRYST1 33.432 65.061 77.176 90.00 90.00 90.00 P 21 21 21 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 0.029911 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015370 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012957 0.00000