+Open data
-Basic information
Entry | Database: PDB / ID: 2azo | ||||||
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Title | DNA MISMATCH REPAIR PROTEIN MUTH FROM E. COLI | ||||||
Components | MUTH | ||||||
Keywords | ENDONUCLEASE / MUTH / DNA REPAIR / HYDROLASE | ||||||
Function / homology | Function and homology information T/G mismatch-specific endonuclease activity / mismatch repair complex / regulation of DNA recombination / DNA modification / mismatch repair / endonuclease activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.3 Å | ||||||
Authors | Yang, W. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. 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 | 2azo.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2azo.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 2azo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2azo_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 2azo_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 2azo_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 2azo_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2azo ftp://data.pdbj.org/pub/pdb/validation_reports/az/2azo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.915447, -0.117429, 0.385006), Vector: Details | ALTHOUGH THERE ARE TWO COPIES OF MUTH IN ONE ASYMMETRIC UNITS, THE COPIES ARE STRUCTURAL DIFFERENT DUE TO CONFORMATIONAL CHANGES BETWEEN TWO SUBDOMAINS IN THE PROTEIN. | |
-Components
#1: Protein | Mass: 25840.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PTX417 / Production host: Escherichia coli (E. coli) / References: UniProt: P06722 #2: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 100MM AMMONIUM ACETATE, 50 MM MAGNESIUM ACETATE, 1 MM DTT AND 12-16 % PEG6000, pH 6.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 20757 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.28→2.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Rsym value: 0.369 / % possible all: 83.8 |
Reflection shell | *PLUS % possible obs: 83.8 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / 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 obs: 0.225 / Rfactor Rfree: 0.289 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3 |