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Yorodumi- PDB-5tk6: Structure of the HD-domain phosphohydrolase OxsA with Oxetanocin-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tk6 | ||||||
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Title | Structure of the HD-domain phosphohydrolase OxsA with Oxetanocin-A diphosphate bound | ||||||
Components | OxsA protein | ||||||
Keywords | METAL BINDING PROTEIN / metalloprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å | ||||||
Authors | Bridwell-Rabb, J. / Drennan, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis. Authors: Bridwell-Rabb, J. / Kang, G. / Zhong, A. / Liu, H.W. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tk6.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tk6.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 5tk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tk6_validation.pdf.gz | 805.5 KB | Display | wwPDB validaton report |
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Full document | 5tk6_full_validation.pdf.gz | 806.4 KB | Display | |
Data in XML | 5tk6_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5tk6_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/5tk6 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/5tk6 | HTTPS FTP |
-Related structure data
Related structure data | 5tk7C 5tk8C 5tk9SC 5tkaC 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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Unit cell |
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-Components
#1: Protein | Mass: 22709.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: oxsA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: O24769 | ||||
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#2: Chemical | #3: Chemical | ChemComp-7D3 / [( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS hydrochloride (pH 8.5), 0.2 M magnesium chloride hexahydrate, 30% w/v PEG 400 soaked in a solution of 3 mM OXT-PP in 30% PEG400 for 1 hour Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→21.41 Å / Num. obs: 15836 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.92→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.699 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TK9 Resolution: 1.924→21.409 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
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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: 1.924→21.409 Å
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Refine LS restraints |
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LS refinement shell |
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