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Yorodumi- PDB-5kah: Crystal structure of a dioxygenase in the Crotonase superfamily i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kah | ||||||
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Title | Crystal structure of a dioxygenase in the Crotonase superfamily in P21, V425T mutant | ||||||
Components | (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / DpgC | ||||||
Function / homology | Function and homology information (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase / enoyl-CoA hydratase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid beta-oxidation / antibiotic biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | Streptomyces toyocaensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.779 Å | ||||||
Authors | Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase. Authors: Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kah.cif.gz | 968.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kah.ent.gz | 807 KB | Display | PDB format |
PDBx/mmJSON format | 5kah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kah_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5kah_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5kah_validation.xml.gz | 178.2 KB | Display | |
Data in CIF | 5kah_validation.cif.gz | 235.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/5kah ftp://data.pdbj.org/pub/pdb/validation_reports/ka/5kah | HTTPS FTP |
-Related structure data
Related structure data | 5kagC 5kajC 2np9S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | ( Mass: 48243.105 Da / Num. of mol.: 12 / Mutation: V425T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8KLK7, (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase #2: Chemical | ChemComp-YE1 / [( #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: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 140 mM ammonium acetate, 14% w/v PEG 4,000, and 100 mM sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.779→39.028 Å / Num. obs: 184721 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.14 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.779→2.83 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NP9 Resolution: 2.779→39.028 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.75 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.779→39.028 Å
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Refine LS restraints |
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LS refinement shell |
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