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Yorodumi- PDB-5kqo: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kqo | ||||||
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Title | 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ussin, N. / 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 | 5kqo.cif.gz | 316.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kqo.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kqo_validation.pdf.gz | 466.1 KB | Display | wwPDB validaton report |
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Full document | 5kqo_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 5kqo_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 5kqo_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/5kqo ftp://data.pdbj.org/pub/pdb/validation_reports/kq/5kqo | HTTPS FTP |
-Related structure data
Related structure data | 5krrC 5krvC 5kryC 5ks1C 1q0lS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 401 / Label seq-ID: 25 - 426
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-Components
#1: Protein | Mass: 46149.750 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 | #3: Chemical | ChemComp-EDO / #4: 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: 3.23 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Sodium citrate/citric acid pH 5.0 1.2 M Ammonium phosphate dibasic 0.2 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 49916 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.7 / CC1/2: 0.948 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q0L Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.491 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.182 / 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: 57.276 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→50 Å
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Refine LS restraints |
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