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- PDB-3rc1: Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura ... -
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Open data
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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 | ||||||
![]() | Sugar 3-ketoreductase | ||||||
![]() | SUGAR BINDING PROTEIN / sugar biosynthesis / ketoreductase / TDP binding / NADP binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holden, H.M. / Kubiak, R.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rbvSC ![]() 3rc2C ![]() 3rc7C ![]() 3rc9C ![]() 3rcbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 384 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/TLO.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TLO.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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