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Yorodumi- PDB-4nmj: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nmj | ||||||
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Title | Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / aldehyde oxidation / NADP reduction / intracellular | ||||||
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: 2.002 Å | ||||||
Authors | Petrova, T. / Boyko, K.M. / Bezsudnova, E.Y. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O. | ||||||
Citation | Journal: To be Published Title: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution Authors: Petrova, T. / Boyko, K.M. / Bezsudnova, E.Y. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / 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 | 4nmj.cif.gz | 801.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nmj.ent.gz | 665.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nmj ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nmj | 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 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): Dlt1270/prare2 References: UniProt: G7VCG0, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-NAP / #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: 3.62 Å3/Da / Density % sol: 65.98 % |
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Crystal grow | Temperature: 291 K / Method: gel-tube counter-diffusion / pH: 7.5 Details: 50 mM HEPES, pH 7.5, 50 mM sodium chloride, 100 mM imidazole, pH 6.5, 1.6 M sodium acetate trihydrate, GEL-TUBE COUNTER-DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 7, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.002→38.09 Å / Num. obs: 418361 / % possible obs: 99.35 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 21.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4H73 Resolution: 2.002→28.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.86 / Stereochemistry target values: Engh & Huber
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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: 2.002→28.09 Å
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Refine LS restraints |
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LS refinement shell |
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