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Yorodumi- PDB-2wox: Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wox | |||||||||
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Title | Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with NAD(P) H-catalytic thiol adduct. | |||||||||
Components | BETAINE ALDEHYDE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE OXIDATION / NADPH COMPLEX | |||||||||
Function / homology | Function and homology information betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / metal ion binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Gonzalez-Segura, L. / Rudino-Pinera, E. / Diaz-Sanchez, A.G. / Munoz-Clares, R.A. | |||||||||
Citation | Journal: Biochem. J. / Year: 2011 Title: Novel NADPH-cysteine covalent adduct found in the active site of an aldehyde dehydrogenase. Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wox.cif.gz | 797.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wox.ent.gz | 662.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wox ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wox | HTTPS FTP |
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-Related structure data
Related structure data | 3zqaC 2wmeS 2xek 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53259.066 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PlysS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase |
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-Non-polymers , 6 types, 1123 molecules
#2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-7PE / #6: Chemical | #7: 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: 3.79 Å3/Da / Density % sol: 67.53 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: CRYSTAL WERE GROWN IN 85 MM HEPES, PH 7.5, 8.5% (V:V) ISOPROPANOL, 17% PEG 4000 AND 2 MM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 9, 2008 Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: ROSENBAUM-ROCK / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 143189 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WME Resolution: 2.3→63.414 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 18.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.565 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→63.414 Å
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Refine LS restraints |
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LS refinement shell |
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