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Yorodumi- PDB-3rc2: Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rc2 | ||||||
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Title | Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP; open conformation | ||||||
Components | Sugar 3-ketoreductase | ||||||
Keywords | SUGAR BINDING PROTEIN / sugar biosynthesis / ketoreductase / NADp binding / TDP binding | ||||||
Function / homology | Function and homology information dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase / D-xylose 1-dehydrogenase (NADP+) activity / D-xylose catabolic process / antibiotic biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Actinomadura kijaniata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Holden, H.M. / Kubiak, R.L. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Combined Structural and Functional Investigation of a C-3''-Ketoreductase Involved in the Biosynthesis of dTDP-l-Digitoxose. Authors: Kubiak, R.L. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rc2.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rc2.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rc2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3rc2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3rc2_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 3rc2_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/3rc2 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/3rc2 | HTTPS FTP |
-Related structure data
Related structure data | 3rbvSC 3rc1C 3rc7C 3rc9C 3rcbC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39262.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura kijaniata (bacteria) / Gene: KijD10 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B3TMR8 |
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-Non-polymers , 7 types, 302 molecules
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-TLO / | ||||
#5: Chemical | ChemComp-NAP / | ||||
#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.0 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM NADP, 5 mM TDP-benzene, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 11, 2011 / Details: montel mirrors |
Radiation | Monochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→84.84 Å / Num. all: 49314 / Num. obs: 49314 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6888 / Rsym value: 0.527 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model generated using binary structure, pdb entry 3RBV Resolution: 1.8→60 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / SU B: 2.513 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.808 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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