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Yorodumi- PDB-5krr: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5krr | ||||||
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Title | 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex with Mn(2+) | ||||||
Components | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Keywords | OXIDOREDUCTASE / Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Function / homology | Function and homology information 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 | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Ussin, N. / Abdulsalam, R.W. / Offermann, L.R. / Perdue, M. / Chruszcz, M. | ||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5krr.cif.gz | 313.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5krr.ent.gz | 255.4 KB | Display | PDB format |
PDBx/mmJSON format | 5krr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5krr_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 5krr_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 5krr_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 5krr_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/5krr ftp://data.pdbj.org/pub/pdb/validation_reports/kr/5krr | HTTPS FTP |
-Related structure data
Related structure data | 5kqoSC 5krvC 5kryC 5ks1C 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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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.) Vibrio vulnificus (strain CMCP6) (bacteria) Strain: CMCP6 / Gene: dxr, VV1_1866 / Plasmid: pJExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q8DBF5, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.36 Å3/Da / Density % sol: 63.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Sodium citrate pH 5.5, 0.8 M Ammonium phosphate, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
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: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 38225 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.917 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5KQO Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.268 / 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: 41.768 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→50 Å
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Refine LS restraints |
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