+Open data
-Basic information
Entry | Database: PDB / ID: 1w4z | ||||||
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Title | Structure of actinorhodin polyketide (actIII) Reductase | ||||||
Components | KETOACYL REDUCTASE | ||||||
Keywords | ANTIBIOTIC BIOSYNTHESIS / TYPE II POLYKETIDE SYNTHESIS / KETOREDUCTASE / SDR / ACP BINDING | ||||||
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: 2.5 Å | ||||||
Authors | Hadfield, A.T. / Limpkin, C. / Teartasin, W. / Simpson, T.J. / Crosby, J. / Crump, M.P. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The Crystal Structure of the Actiii Actinorhodin Polyketide Reductase; Proposed Mechanism for Acp and Polyketide Binding Authors: Hadfield, A.T. / Limpkin, C. / Teartasin, W. / Simpson, T.J. / Crosby, J. / Crump, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w4z.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4z.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 1w4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4z ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4z | HTTPS FTP |
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-Related structure data
Related structure data | 1edoS 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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Unit cell |
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-Components
#1: Protein | Mass: 29464.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A3(2) / M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | Sequence details | MODIFIED BY ADDITION OF N-TERMINAL HIS TAG | |
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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: 3.3 Å3/Da / Density % sol: 62.5 % |
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Crystal grow | Details: MOTHER LIQUOR 5 MG ML-1 PROTEIN AND 5 MM NADP IN 25 MM PHOSPHATE BUFFER PH 8 WITH 10%(V/V) GLYCEROL RESERVOIR SOLUTION 4.0-4.4 M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 25371 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.5→30 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDO Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.82 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES B203-B209 WERE DISORDERED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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