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Yorodumi- PDB-1eyy: CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eyy | |||||||||
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Title | CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI. | |||||||||
Components | ALDEHYDE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / NUCLEOTIDE BINDING DOMAIN | |||||||||
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 / MIR, MAD / Resolution: 2.5 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 | 1eyy.cif.gz | 377.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyy.ent.gz | 309.6 KB | Display | PDB format |
PDBx/mmJSON format | 1eyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eyy_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1eyy_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1eyy_validation.xml.gz | 73.3 KB | Display | |
Data in CIF | 1eyy_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyy ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyy | HTTPS FTP |
-Related 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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-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 / | Nonpolymer details | ONLY THE ADENINE, RIBOSE AND PYROPHOSPHATE PORTION of NADP+ WERE VISIBLE IN ELECTRON DENSITY WITH ...ONLY THE ADENINE, RIBOSE AND PYROPHOSPH | Sequence details | THE STRUCTURE WAS REFINED AS A SELENOMETHIONINE MUTANT. IN THE COORDINATE FILE WHICH WE HAVE ...THE STRUCTURE WAS REFINED AS A SELENOMETH | |
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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: 2.22 Å3/Da / Density % sol: 44.6 % | ||||||||||||||||||||
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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: X12C / Wavelength: 0.980269 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Jul 24, 1997 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980269 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→45.2 Å / Num. all: 172343 / Num. obs: 130457 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 1.67 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.48→2.57 Å / Redundancy: 1.622 % / Rmerge(I) obs: 0.118 / Num. unique all: 12664 / % possible all: 95.3 |
Reflection | *PLUS Num. measured all: 218666 |
Reflection shell | *PLUS % possible obs: 95.3 % / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR, MAD / Resolution: 2.5→25.77 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 3708752.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: NAP occupancy set to 0.5
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Solvent computation | Solvent model: flat model / Bsol: 15.5085 Å2 / ksol: 0.349587 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→25.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / 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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