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- PDB-5kry: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kry | ||||||
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Title | 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus | ||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Function / homology | ![]() isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / manganese ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ussin, N. / Abdulsalam, R.W. / Chruszcz, M. | ||||||
![]() | ![]() Title: Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. Authors: Ussin, N.K. / Bagnell, A.M. / Offermann, L.R. / Abdulsalam, R. / Perdue, M.L. / Magee, P. / Chruszcz, 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 | ![]() | 316.6 KB | Display | ![]() |
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PDB format | ![]() | 259.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.2 KB | Display | ![]() |
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Full document | ![]() | 445 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kqoSC ![]() 5krrC ![]() 5krvC ![]() 5ks1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43591.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CMCP6 / Gene: dxr, VV1_1866 / Plasmid: pJExpress411 / Production host: ![]() ![]() References: UniProt: Q8DBF5, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% w/v PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 53399 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.859 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KQO Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.587 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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