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Yorodumi- PDB-5yvm: Crystal Structure of the archaeal halo-thermophilic Red Sea brine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yvm | ||||||
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Title | Crystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NZQ | ||||||
Components | alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / protein-cofactor complex / dehydrogenase / NZQ / 5S6S-NADPH(OH)2 / halophilic / thermophilic | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | candidate divison MSBL1 archaeon SCGC-AAA259E19 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Model details | ADH/D1 bound to manganese and 5S,6S-NADPH(OH)2 (NZQ) | ||||||
Authors | Groetzinger, S.W. / Strillinger, E. / Frank, A. / Eppinger, J. / Groll, M. / Arold, S.T. | ||||||
Funding support | Saudi Arabia, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes Authors: Groetzinger, S.W. / Karan, R. / Strillinger, E. / Bader, S. / Frank, A. / Al Rowaihi, I.S. / Akal, A. / Wackerow, W. / Archer, J.A. / Rueping, M. / Weuster-Botz, D. / Groll, M. / Eppinger, J. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yvm.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yvm.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yvm ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yvm | HTTPS FTP |
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-Related structure data
Related structure data | 5yvrC 5yvsC 3bfjS 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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Unit cell |
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-Components
#1: Protein | Mass: 44368.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) candidate divison MSBL1 archaeon SCGC-AAA259E19 (archaea) Gene: AKJ65_00115 / Plasmid: pTA963 / Production host: Haloferax volcanii (archaea) / Strain (production host): H1895 / References: UniProt: A0A133UP32 |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-NZQ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 150mM Mg Acetate, 27% methyl-pentane-diol, 100mM Na cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→48.092 Å / Num. obs: 21120 / % possible obs: 96 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.068 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2104 / CC1/2: 0.84 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3bfj Resolution: 2.12→48.092 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.36 Å2 / Biso mean: 56.0437 Å2 / Biso min: 27.56 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.12→48.092 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 19.3309 Å / Origin y: 12.4659 Å / Origin z: 46.7351 Å
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Refinement TLS group |
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