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Yorodumi- PDB-5eeb: Apo form of thermostable aldehyde dehydrogenase from Pyrobaculum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eeb | ||||||
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Title | Apo form of thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Thermostable aldehyde dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | Pyrobaculum ferrireducens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.038 Å | ||||||
Authors | Petrova, T.E. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O. | ||||||
Citation | Journal: Archaea / Year: 2016 Title: NADP-Dependent Aldehyde Dehydrogenase from ArchaeonPyrobaculum sp.1860: Structural and Functional Features. Authors: Bezsudnova, E.Y. / Petrova, T.E. / Artemova, N.V. / Boyko, K.M. / Shabalin, I.G. / Rakitina, T.V. / Polyakov, K.M. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eeb.cif.gz | 708.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eeb.ent.gz | 595.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5eeb ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5eeb | HTTPS FTP |
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-Related structure data
Related structure data | 5ek6C 5euyC 5exfC 5f2cC 4h73S 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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Unit cell |
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-Components
#1: Protein | Mass: 54459.207 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum ferrireducens (archaea) / Gene: P186_1147 / Production host: Escherichia coli (E. coli) / Strain (production host): Dlt1270/prare2 / References: UniProt: G7VCG0 |
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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: 3.61 Å3/Da / Density % sol: 65.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, NaCl, beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.984 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3.038→29.771 Å / Num. obs: 120589 / % possible obs: 98.94 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.266 / Net I/σ(I): 7.71 |
Reflection shell | Resolution: 3.038→3.2 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H73 Resolution: 3.038→29.771 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.32 / 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: 3.038→29.771 Å
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Refine LS restraints |
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LS refinement shell |
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