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Yorodumi- PDB-1ez0: CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ez0 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI. | |||||||||
Components | ALDEHYDE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / Nucleotide binding domain / NADP+ | |||||||||
Function / homology | Function and homology information aldehyde dehydrogenase (NADP+) / aldehyde dehydrogenase (NADP+) activity Similarity search - Function | |||||||||
Biological species | Vibrio harveyi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 Å | |||||||||
Authors | Ahvazi, B. / Coulombe, R. / Delarge, M. / Vedadi, M. / Zhang, L. / Meighen, E. / Vrielink, A. | |||||||||
Citation | Journal: Biochem.J. / Year: 2000 Title: Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity. Authors: Ahvazi, B. / Coulombe, R. / Delarge, M. / Vedadi, M. / Zhang, L. / Meighen, E. / Vrielink, A. #1: Journal: Protein Sci. / Year: 1996 Title: Crystallization and Preliminary X-ray Analysis of Aldehyde Dehydrogenase from Vibrio harveyi Authors: Croteau, N. / Vedadi, M. / Delarge, M. / Meighen, E. / Abu-Abed, M. / Howell, P.L. / Vrielink, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ez0.cif.gz | 385.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ez0.ent.gz | 315.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ez0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/1ez0 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/1ez0 | HTTPS FTP |
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-Related structure data
Related structure data | 1eyySC 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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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 54509.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: B392 / Gene: ALDH / Plasmid: PT7-3 / Gene (production host): ALDH / Production host: Escherichia coli (E. coli) / Strain (production host): K38 References: UniProt: Q56694, aldehyde dehydrogenase [NAD(P)+] #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: 2.21 Å3/Da / Density % sol: 44.25 % | ||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, Sodium acetate, Sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||
Crystal grow | *PLUS Details: Croteau, N., (1996) Protein Sci., 5, 2130. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072021 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072021 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 175195 / Num. obs: 92467 / % possible obs: 83.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.89 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.051 / Num. unique all: 8082 / % possible all: 73.7 |
Reflection | *PLUS Num. measured all: 189982 |
Reflection shell | *PLUS % possible obs: 73.7 % / Mean I/σ(I) obs: 17.2 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 1eyy Resolution: 2.1→26.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2617344.74 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 46.2429 Å2 / ksol: 0.407586 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→26.44 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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