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Yorodumi- PDB-6zy0: Catabolic reductive dehalogenase NpRdhA, N-terminally tagged, K48... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zy0 | ||||||
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Title | Catabolic reductive dehalogenase NpRdhA, N-terminally tagged, K488Q variant | ||||||
Components | Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein | ||||||
Keywords | OXIDOREDUCTASE / reductive dehalogenase / B12 / iron-sulfur | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nitratireductor pacificus pht-3B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.13 Å | ||||||
Authors | Leys, D. / Halliwell, T. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Microorganisms / Year: 2020 Title: Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Authors: Halliwell, T. / Fisher, K. / Payne, K.A.P. / Rigby, S.E.J. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zy0.cif.gz | 510.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zy0.ent.gz | 336.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zy0 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zy0 | HTTPS FTP |
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-Related structure data
Related structure data | 6zxuSC 6zxxC 6zy1C 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 79721.516 Da / Num. of mol.: 3 / Mutation: K488Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratireductor pacificus pht-3B (bacteria) Gene: NA2_14372 / Production host: Bacillus megaterium (bacteria) / References: UniProt: K2MB66 |
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-Non-polymers , 5 types, 345 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane (pH 8.5), 0.2 M sodium nitrate and 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→106.66 Å / Num. obs: 84101 / % possible obs: 94.5 % / Redundancy: 7 % / Biso Wilson estimate: 34.23 Å2 / CC1/2: 1 / Rrim(I) all: 0.196 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.13→2.44 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4206 / CC1/2: 0.6 / Rrim(I) all: 1.238 / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6ZXU Resolution: 2.13→106.66 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.658 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 37.27 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→106.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.44 Å
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