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Yorodumi- PDB-4cvb: Crystal structure of quinone-dependent alcohol dehydrogenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cvb | ||||||
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Title | Crystal structure of quinone-dependent alcohol dehydrogenase from Pseudogluconobacter saccharoketogenenes | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / CARBOHYDRATE OXIDATION / QUINOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOGLUCONOBACTER SACCHAROKETOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Rozeboom, H.J. / Yu, S. / Mikkelsen, R. / Nikolaev, I. / Mulder, H. / Dijkstra, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase from Pseudogluconobacter Saccharoketogenes. A Versatile Dehydrogenase Oxidizing Alcohols and Carbohydrates. Authors: Rozeboom, H.J. / Yu, S. / Mikkelsen, R. / Nikolaev, I. / Mulder, H.J. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cvb.cif.gz | 233.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvb.ent.gz | 185.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvb ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvb | HTTPS FTP |
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-Related structure data
Related structure data | 4cvcC 1kb0S 1yiqS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61363.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-608 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOGLUCONOBACTER SACCHAROKETOGENES (bacteria) Strain: IFO 14464 / Plasmid: PPIC2-ADH / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115 References: UniProt: Q93RE9, alcohol dehydrogenase (cytochrome c) |
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-Non-polymers , 6 types, 634 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-PQQ / | ||||||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PPI / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | N-TERMINUS OF MATURE PROTEIN STARTS AT POSITION 37 (AEPSK.. ) |
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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7 Details: 18-21% PEG550 MME, 20 MM ZN(AC)2, 100 MM PCB BUFFER PH 6-7 |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 | |||||||||||||||
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 2, 2009 / Details: OXMIC MIRRORS | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.72→30.5 Å / Num. obs: 59031 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4 | |||||||||||||||
Reflection shell | Resolution: 1.72→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.3 / % possible all: 31.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1KB0 AND 1YIQ Resolution: 1.72→27.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.035 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.709 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→27.95 Å
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Refine LS restraints |
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