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Yorodumi- PDB-1bxz: CRYSTAL STRUCTURE OF A THERMOPHILIC ALCOHOL DEHYDROGENASE SUBSTRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bxz | ||||||
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Title | CRYSTAL STRUCTURE OF A THERMOPHILIC ALCOHOL DEHYDROGENASE SUBSTRATE COMPLEX FROM THERMOANAEROBACTER BROCKII | ||||||
Components | NADP-DEPENDENT ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / THERMOPHILIC ALCOHOL DEHYDROGENASE | ||||||
Function / homology | Function and homology information isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacter brockii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Li, C. / Heatwole, J. / Soelaiman, S. / Shoham, M. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Crystal structure of a thermophilic alcohol dehydrogenase substrate complex suggests determinants of substrate specificity and thermostability. Authors: Li, C. / Heatwole, J. / Soelaiman, S. / Shoham, M. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystal Parameters of an Alcohol Dehydrogenase from the Extreme Thermophile Thermoanaerobium Brockii Authors: Zhang, Z. / Djebli, A. / Shoham, M. / Frolow, F. / Peretz, M. / Burstein, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bxz.cif.gz | 271.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bxz.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bxz_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 1bxz_full_validation.pdf.gz | 514.6 KB | Display | |
Data in XML | 1bxz_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 1bxz_validation.cif.gz | 80.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bxz ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bxz | HTTPS FTP |
-Related structure data
Related structure data | 1kevS 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 domain:
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37694.871 Da / Num. of mol.: 4 / Fragment: NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14941, alcohol dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 264 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-SBT / #6: 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: 2.77 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996 |
Radiation | Monochromator: CRYSTAL MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 30323 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.083 / Rsym value: 0.079 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.99→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.278 / % possible all: 89 |
Reflection shell | *PLUS % possible obs: 89 % / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KEV Resolution: 2.99→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 41.89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.99→50 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.99→3.01 Å / Num. reflection Rwork: 604 / Total num. of bins used: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 29745 / Num. reflection Rfree: 2575 / Rfactor obs: 0.214 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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