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Yorodumi- PDB-8dq5: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dq5 | ||||||
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Title | X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase T191I variant | ||||||
Components | Ribonucleoside-diphosphate reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Flavobacterium johnsoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rose, H.R. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase T191I variant Authors: Rose, H.R. / Boal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dq5.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dq5.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 8dq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dq5 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dq5 | HTTPS FTP |
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-Related structure data
Related structure data | 6cwpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39909.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A5FCJ5, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.2 M Mg-acetate, 20% (v/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36014 / % possible obs: 98.5 % / Redundancy: 5.5 % / CC1/2: 0.899 / Rpim(I) all: 0.042 / Net I/σ(I): 18.76 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1964 / CC1/2: 0.678 / Rpim(I) all: 0.387 / Rrim(I) all: 0.853 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CWP Resolution: 2.1→46.57 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 31.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.12 Å2 / Biso mean: 30.5147 Å2 / Biso min: 2.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.57 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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