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- PDB-5f2c: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f2c | ||||||
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Title | Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 crystallized in microgravity (complex with NADP+) | ||||||
![]() | Aldehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Thermostable aldehyde dehydrogenase | ||||||
Function / homology | ![]() oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petrova, T.E. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 821.3 KB | Display | ![]() |
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PDB format | ![]() | 682.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.5 MB | Display | ![]() |
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Full document | ![]() | 5.5 MB | Display | |
Data in XML | ![]() | 166.5 KB | Display | |
Data in CIF | ![]() | 241.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eebC ![]() 5ek6C ![]() 5euyC ![]() 5exfC ![]() 4h73S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystallization details 50 mM HEPES pH 7.5; 50 mM NaCl; 100 mM Imidazole pH 6.5; 1.6M Sodium acetate trihydrate. The crystal was grown in a microgravity environment. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→29.145 Å / Num. all: 4133317 / Num. obs: 493450 / % possible obs: 87.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.898→1.9193 Å / % possible all: 22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H73 Resolution: 1.898→29.145 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.08 / 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: 1.898→29.145 Å
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Refine LS restraints |
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LS refinement shell |
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