[English] 日本語
Yorodumi- PDB-4cvc: Crystal structure of quinone-dependent alcohol dehydrogenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cvc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of quinone-dependent alcohol dehydrogenase from Pseudogluconobacter saccharoketogenenes with zinc in the active site | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / CARBOHYDRATE OXIDATION / QUINOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOGLUCONOBACTER SACCHAROKETOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cvc.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cvc.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvc ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvc | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cvbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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) |
---|
-Non-polymers , 6 types, 582 molecules
#2: Chemical | ChemComp-PEG / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-PQQ / | ||||||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PPI / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 18-21% PEG550, 20 MM ZN(AC)2, 100 MM PCB BUFFER PH 6-7, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→36 Å / Num. obs: 54822 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.84→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.2 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CVB Resolution: 1.83→72.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.726 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→72.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|