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- PDB-5ks1: 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: 5ks1 | ||||||
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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. / Offermann, L.R. / 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 | ![]() | 318.4 KB | Display | ![]() |
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PDB format | ![]() | 260.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kqoSC ![]() 5krrC ![]() 5krvC ![]() 5kryC 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
#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: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Sodium citrate pH 5.0, 0.8 M Ammonium phosphate, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 46042 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.934 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KQO Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.209 / 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: 88.721 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50 Å
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Refine LS restraints |
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