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- PDB-8vr2: Crystal structure of the Pcryo_0617 oxidoreductase/decarboxylase ... -
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Open data
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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 | ||||||
![]() | NAD-dependent epimerase/dehydratase | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bockhaus, N.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269.5 KB | Display | ![]() |
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PDB format | ![]() | 215.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 50.2 KB | Display | |
Data in CIF | ![]() | 70.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vr3C ![]() 8vr5C ![]() 8vr6C ![]() 8vr7C ![]() 8vrmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() Gene: Pcryo_0617 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 497 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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Refine LS restraints |
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