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Yorodumi- PDB-1r0k: Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r0k | ||||||
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Title | Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis | ||||||
Components | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Keywords | OXIDOREDUCTASE / reductoisomerase / NADPH dependent / Fosmidomycin / non-mevalonate pathway / zymomonas mobilis | ||||||
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 | Zymomonas mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Ricagno, S. / Grolle, S. / Bringer-Meyer, S. / Sahm, H. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2004 Title: Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase from Zymomonas mobilis at 1.9-A resolution. Authors: Ricagno, S. / Grolle, S. / Bringer-Meyer, S. / Sahm, H. / Lindqvist, Y. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r0k.cif.gz | 314.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r0k.ent.gz | 254.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r0k_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 1r0k_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 1r0k_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 1r0k_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/1r0k ftp://data.pdbj.org/pub/pdb/validation_reports/r0/1r0k | HTTPS FTP |
-Related structure data
Related structure data | 1r0lC 1jvsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41890.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: DXR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 [pREP4] References: UniProt: Q9X5F2, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | ChemComp-ACT / #3: 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: 2.4 Å3/Da / Density % sol: 48.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Na citrate, PEG 4000, Ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2001 |
Radiation | Monochromator: Premirror, Triangular monochromator, Bent mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8452 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→29.63 Å / Num. all: 118460 / Num. obs: 118460 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 12.4 Å2 / Limit h max: 45 / Limit h min: -45 / Limit k max: 48 / Limit k min: -45 / Limit l max: 51 / Limit l min: 0 / Observed criterion F max: 2499288.66 / Observed criterion F min: 22.3 / Rsym value: 0.083 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique all: 19549 / Rsym value: 0.42 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JVS, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (E.coli) Resolution: 1.91→29.63 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 50.4225 Å2 / ksol: 0.347591 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.74 Å2 / Biso mean: 20.63 Å2 / Biso min: 6.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.91→29.63 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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