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Yorodumi- PDB-4jlw: Crystal structure of formaldehyde dehydrogenase from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jlw | ||||||
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Title | Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa | ||||||
Components | Glutathione-independent formaldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Zinc Finger / dehydrogenase / NAD+ Binding / Zinc Binding | ||||||
Function / homology | Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Chen, S. / Liao, Y.P. / Wang, D.L. / Wang, S. / Ding, J.F. / Wang, Y.M. / Cai, L.J. / Ran, X.Y. / Zhu, H.X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa: the binary complex with the cofactor NAD+. Authors: Liao, Y.P. / Chen, S. / Wang, D.L. / Zhang, W. / Wang, S. / Ding, J.F. / Wang, Y.M. / Cai, L.J. / Ran, X.Y. / Wang, X. / Zhu, H.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jlw.cif.gz | 587.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jlw.ent.gz | 490 KB | Display | PDB format |
PDBx/mmJSON format | 4jlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jlw_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4jlw_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4jlw_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 4jlw_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jlw ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jlw | HTTPS FTP |
-Related structure data
Related structure data | 1kolS 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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-Components
#1: Protein | Mass: 42057.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: LESB58 / Gene: fdhA, PLES_58161 / Plasmid: pCold II / Production host: Escherichia coli (E. coli) / Strain (production host): pG-Tf2 / References: UniProt: B7V5W2 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-SO4 / #5: 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: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis-Tris, 1.8M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2011 |
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 47323 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.203 / Net I/σ(I): 6.43 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.91 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KOL Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.865 / SU B: 28.45 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.159 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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