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Yorodumi- PDB-3rc1: Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rc1 | ||||||
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Title | Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata incomplex with NADP and TDP-benzene | ||||||
Components | Sugar 3-ketoreductase | ||||||
Keywords | SUGAR BINDING PROTEIN / sugar biosynthesis / ketoreductase / TDP binding / NADP binding | ||||||
Function / homology | Function and homology information dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase / antibiotic biosynthetic process / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Actinomadura kijaniata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 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 | 3rc1.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rc1.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/3rc1 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/3rc1 | HTTPS FTP |
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-Related structure data
Related structure data | 3rbvSC 3rc2C 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, 384 molecules
#2: Chemical | ChemComp-PO4 / | ||
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#3: Chemical | ChemComp-TLO / | ||
#4: Chemical | ChemComp-NAP / | ||
#5: Chemical | ChemComp-NA / | ||
#6: Chemical | ChemComp-EDO / | ||
#7: Chemical | #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: 3.51 Å3/Da / Density % sol: 64.94 % |
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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 12, 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: 1.71→84.65 Å / Num. all: 59618 / Num. obs: 59618 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.71→1.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.5 / Num. unique all: 8171 / Rsym value: 0.643 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model generated from binary structure, PDB entry 3RBV Resolution: 1.71→60 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.826 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095 / 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: 20.572 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.756 Å / Total num. of bins used: 20
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