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Yorodumi- PDB-8vr2: Crystal structure of the Pcryo_0617 oxidoreductase/decarboxylase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vr2 | ||||||
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Title | Crystal structure of the Pcryo_0617 oxidoreductase/decarboxylase from Psychrobacter cryohalolentis K5 in the presence of NAD and UDP | ||||||
Components | NAD-dependent epimerase/dehydratase | ||||||
Keywords | OXIDOREDUCTASE / psychrobacter / 2 / 3 / 4-trideoxy-l-arabinose | ||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / NAD-dependent epimerase/dehydratase Function and homology information | ||||||
Biological species | Psychrobacter cryohalolentis K5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Bockhaus, N.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5 Authors: Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vr2.cif.gz | 269.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vr2.ent.gz | 215.8 KB | Display | PDB format |
PDBx/mmJSON format | 8vr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vr2 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vr2 | HTTPS FTP |
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-Related structure data
Related structure data | 8vr3C 8vr5C 8vr6C 8vr7C 8vrmC C: citing same article (ref.) |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36807.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria) Gene: Pcryo_0617 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD53 |
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-Non-polymers , 5 types, 497 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-UDP / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-MES / | #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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein incubated with 5 mM UDP and 5 mM NAD. Precipitant: 16-20% PEG 5000, 200 mM tetramethylammonium chloride, and 100 mM MES (pH 6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 137349 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.081 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9174 / Rsym value: 0.346 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→48.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.642 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.058 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→48.95 Å
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