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Yorodumi- PDB-1h2b: Crystal Structure of the Alcohol Dehydrogenase from the Hyperther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h2b | ||||||
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Title | Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ARCHAEA / HYPERTHERMOPHILE / ALCOHOL DEHYDROGENASE OXIDOREDUCTASE / ZINC | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / nucleotide binding / zinc ion binding Similarity search - Function | ||||||
Biological species | AEROPYRUM PERNIX (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å | ||||||
Authors | Guy, J.E. / Isupov, M.N. / Littlechild, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix. Authors: Guy, J.E. / Isupov, M.N. / Littlechild, J.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum Pernix. Authors: Guy, J.E. / Isupov, M.N. / Littlechild, J.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2b.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2b.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2b ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2b | HTTPS FTP |
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-Related structure data
Related structure data | 1hszS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.11131, 0.99372, 0.0112), Vector: |
-Components
#1: Protein | Mass: 39620.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AEROPYRUM PERNIX (archaea) / Plasmid: PTRC 99 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9Y9P9, alcohol dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Compound details | BIOLOGICAL | |
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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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.75 / Details: pH 6.75 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0704 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2002 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0704 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→15 Å / Num. obs: 1008062 / % possible obs: 97.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.62→1.65 Å / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.52 / % possible all: 95.6 |
Reflection | *PLUS Highest resolution: 1.62 Å / Lowest resolution: 15 Å / Num. obs: 88078 / Redundancy: 11.7 % / Rmerge(I) obs: 0.054 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1HSZ Resolution: 1.62→15 Å / SU B: 1.546 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088
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Displacement parameters | Biso mean: 25.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→15 Å
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Refinement | *PLUS Rfactor Rfree: 0.2033 / Rfactor Rwork: 0.168 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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