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Yorodumi- PDB-5kcm: Crystal structure of iron-sulfur cluster containing photolyase Ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcm | ||||||
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Title | Crystal structure of iron-sulfur cluster containing photolyase PhrB mutant I51W | ||||||
Components | (6-4) photolyase | ||||||
Keywords | LYASE / (6-4) Photolyase / Mutant / (6-4) Photorepair / FeS-BCP | ||||||
Function / homology | Function and homology information (6-4)DNA photolyase / DNA (6-4) photolyase activity / photoreactive repair / FAD binding / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å | ||||||
Authors | Yang, X. / Bowatte, K. / Zhang, F. / Lamparter, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Photochem. Photobiol. / Year: 2017 Title: Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Authors: Zhang, F. / Ma, H. / Bowatte, K. / Kwiatkowski, D. / Mittmann, E. / Qasem, H. / Krau, N. / Zeng, X. / Ren, Z. / Scheerer, P. / Yang, X. / Lamparter, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kcm.cif.gz | 456.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kcm.ent.gz | 372.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcm ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcm | HTTPS FTP |
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-Related structure data
Related structure data | 5lfaC 4djaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 59296.922 Da / Num. of mol.: 2 / Mutation: I51W Source method: isolated from a genetically manipulated source Details: FAD and SF4 are ligands Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: phrB, Atu4765 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CH39, (6-4)DNA photolyase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 5% PEG 400 0.1 M MES at pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→44.655 Å / Num. obs: 65431 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 11.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DJA Resolution: 2.149→44.655 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.149→44.655 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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