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Yorodumi- PDB-1n5q: Crystal structure of a Monooxygenase from the gene ActVA-Orf6 of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n5q | ||||||
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Title | Crystal structure of a Monooxygenase from the gene ActVA-Orf6 of Streptomyces coelicolor in complex with dehydrated Sancycline | ||||||
Components | ActaVA-Orf6 monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase / aromatic polyketides / actinorhodin / dihydrokalafungin / sancycline / streptomyces coelicolor | ||||||
Function / homology | Function and homology information ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / fourier difference / Resolution: 1.74 Å | ||||||
Authors | Sciara, G. / Kendrew, S.G. / Miele, A.E. / Marsh, N.G. / Federici, L. / Malatesta, F. / Schimperna, G. / Savino, C. / Vallone, B. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis Authors: Sciara, G. / Kendrew, S.G. / Miele, A.E. / Marsh, N.G. / Federici, L. / Malatesta, F. / Schimperna, G. / Savino, C. / Vallone, B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary X-ray diffraction studies of a monooxygenase from Streptomyces coelicolor A3(2) involved in the biosynthesis of the polyketide actinorhodin Authors: Kendrew, S.G. / Federici, L. / Savino, C. / Miele, A.E. / Marsh, N.G. / Vallone, B. #2: Journal: J.Bacteriol. / Year: 1997 Title: Identification of a monooxygenase from Streptomyces coelicolor A3(2) involved in the biosynthesis of actinorhodin: purification and characterization of the recombinant enzyme Authors: Kendrew, S.G. / Hopwood, D.A. / Marsh, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n5q.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n5q.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n5q_validation.pdf.gz | 953.3 KB | Display | wwPDB validaton report |
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Full document | 1n5q_full_validation.pdf.gz | 961.2 KB | Display | |
Data in XML | 1n5q_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1n5q_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5q ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5q | HTTPS FTP |
-Related structure data
Related structure data | 1lq9SC 1n5sC 1n5tC 1n5vC 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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Details | The biological unit is a dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 11978.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: ActVA-Orf6 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53908 #2: Chemical | ChemComp-P6G / | #3: Chemical | ChemComp-TNC / | #4: 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: 1.87 Å3/Da / Density % sol: 33.86 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion + soaking / pH: 7 Details: ammonium sulfate, PEG 200, Tris or Hepes buffer, pH 7.0, vapour diffusion + soaking, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 5, 2000 / Details: Three-segment Pt-coated toroidal mirror |
Radiation | Monochromator: Double crystal (Si111,Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→15 Å / Num. all: 21456 / Num. obs: 21456 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.74→1.77 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1057 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 118991 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: fourier difference Starting model: PDB ENTRY 1LQ9 Resolution: 1.74→15 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.74→15 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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