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Yorodumi- PDB-1bkn: CRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COLI DNA M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bkn | ||||||
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Title | CRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COLI DNA MISMATCH REPAIR PROTEIN MUTL | ||||||
Components | MUTL | ||||||
Keywords | DNA REPAIR / ATPASE / DNA BINDING | ||||||
Function / homology | Function and homology information single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.9 Å | ||||||
Authors | Yang, W. / Ban, C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis. Authors: Ban, C. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bkn.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bkn.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bkn_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 1bkn_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 1bkn_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 1bkn_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkn ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.041784, 0.989309, -0.139721), Vector: |
-Components
#1: Protein | Mass: 39299.602 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 40KD FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: MUTL / Plasmid: PTX418 / Gene (production host): MUTL / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (LAMBDA DE3) / References: UniProt: P23367 #2: Water | ChemComp-HOH / | Sequence details | THE FIRST THREE RESIDUES IN THE SEQUENCE ARE NOT ENCODED BY E. COLI MUTL GENE. THEY ARE FUSED INTO ...THE FIRST THREE RESIDUES IN THE SEQUENCE ARE NOT ENCODED BY E. COLI MUTL GENE. THEY ARE FUSED INTO MUTL PROTEIN DUE TO CLONING AND EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % Description: DATA TO 2.9A ARE USED FOR THE STRUCTURE REFINEMENT. THE LAST SHELL (2.9A TO 3.0A) HAS RSYM OF 0.50, COMPLETENESS OF 98.3% AND I/SIGI OF 2.1. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 / Details: pH 6.6 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 23519 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 84.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.7 / % possible all: 84.6 |
Reflection | *PLUS Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 84.6 % / Rmerge(I) obs: 0.696 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 73.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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