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Yorodumi- PDB-5ekc: Thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ekc | ||||||
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Title | Thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 complexed with NADP+ | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Aldehyde dehydrogenase / thermostable | ||||||
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 sp. 1860 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å | ||||||
Authors | Petrova, T. / Bezsudnova, E.Y. / Boyko, K.M. / Nikolaeva, A.Y. / Rakitina, T.V. / Shabalin, I.G. / Popov, V.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Structure of thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 complexed with NADP+ Authors: Bezsudnova, E.Y. / Petrova, T.E. / Rakitina, T.V. / Boyko, K.M. / Nikolaeva, A.Y. / Polyakov, K.M. / Shabalin, I.G. / 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 | 5ekc.cif.gz | 789.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ekc.ent.gz | 653 KB | Display | PDB format |
PDBx/mmJSON format | 5ekc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/5ekc ftp://data.pdbj.org/pub/pdb/validation_reports/ek/5ekc | HTTPS FTP |
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-Related structure data
Related structure data | 4h73S S: Starting model for refinement |
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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 sp. 1860 (archaea) / Gene: P186_1147 / Production host: Escherichia coli (E. coli) / Variant (production host): Dlt1270/prare2 / References: UniProt: G7VCG0 #2: Chemical | ChemComp-NAP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES 0.05 M, pH=7.5 NaCl 0.05 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.895→49.646 Å / Num. obs: 492441 / % possible obs: 98.55 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.895→1.92 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.8 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H73 Resolution: 1.895→49.646 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.45 / 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: 1.895→49.646 Å
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Refine LS restraints |
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LS refinement shell |
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