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Yorodumi- PDB-5uwz: Protein 12 with aldehyde deformylating oxygenase activity from Gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uwz | ||||||
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Title | Protein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus | ||||||
Components | Aldehyde decarbonylase | ||||||
Keywords | LYASE / decarbonylase / iron / ferritin | ||||||
Function / homology | Function and homology information aldehyde oxygenase (deformylating) / : / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å | ||||||
Authors | Wilson, D.K. | ||||||
Citation | Journal: To Be Published Title: Protein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uwz.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uwz.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 5uwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uwz_validation.pdf.gz | 680.5 KB | Display | wwPDB validaton report |
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Full document | 5uwz_full_validation.pdf.gz | 682.5 KB | Display | |
Data in XML | 5uwz_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 5uwz_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwz ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwz | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 27402.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria) Strain: PCC 7421 / Gene: gll3146 / Production host: Escherichia coli (E. coli) References: UniProt: Q7NGM3, aldehyde oxygenase (deformylating) | ||||
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#2: Chemical | #3: Chemical | ChemComp-STE / | #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: 2.39 Å3/Da / Density % sol: 48.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 10% PEG 3000, 100 mM citrate, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03317 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→56.4 Å / Num. obs: 73111 / % possible obs: 99.7 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.25→1.27 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Resolution: 1.25→56.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.087 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.842 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→56.36 Å
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Refine LS restraints |
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