+Open data
-Basic information
Entry | Database: PDB / ID: 1x7h | ||||||
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Title | Actinorhodin Polyketide Ketoreductase, with NADPH bound | ||||||
Components | Putative ketoacyl reductase | ||||||
Keywords | OXIDOREDUCTASE / polyketide / actinorhodin / ketoreductase / combinatorial biosynthesis / short chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / antibiotic biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Korman, T.P. / Hill, J.A. / Vu, T.N. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural analysis of actinorhodin polyketide ketoreductase: cofactor binding and substrate specificity Authors: Korman, T.P. / Hill, J.A. / Vu, T.N. / Tsai, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x7h.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x7h.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 1x7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/1x7h ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x7h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | he second part of the biological assembly is generated by the two fold axis: X-Y, -Y, 1/3-Z |
-Components
#1: Protein | Mass: 27293.014 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: CH999 / Gene: actIII / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #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: 4.76 Å3/Da / Density % sol: 74.14 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004 / Details: mirrors |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 39267 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.092 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 1.75 / Rsym value: 0.687 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 79761.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2207 Å2 / ksol: 0.390891 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→47.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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