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Yorodumi- PDB-5wqo: Crystal structure of a carbonyl reductase from Pseudomonas aerugi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wqo | ||||||||||||
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Title | Crystal structure of a carbonyl reductase from Pseudomonas aeruginosa PAO1 in complex with NADP (condition I) | ||||||||||||
Components | Probable dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / short chain dehydrogenase / reductase | ||||||||||||
Function / homology | Function and homology information carbonyl reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||||||||
Authors | Li, S. / Wang, Y. / Bartlam, M. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: FEBS Lett. / Year: 2017 Title: Structure and characterization of a NAD(P)H-dependent carbonyl reductase from Pseudomonas aeruginosa PAO1. Authors: Li, S. / Teng, X. / Su, L. / Mao, G. / Xu, Y. / Li, T. / Liu, R. / Zhang, Q. / Wang, Y. / Bartlam, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wqo.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wqo.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wqo_validation.pdf.gz | 813.9 KB | Display | wwPDB validaton report |
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Full document | 5wqo_full_validation.pdf.gz | 816.4 KB | Display | |
Data in XML | 5wqo_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 5wqo_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/5wqo ftp://data.pdbj.org/pub/pdb/validation_reports/wq/5wqo | HTTPS FTP |
-Related structure data
Related structure data | 5wqmSC 5wqnC 5wqpC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 229 / Label seq-ID: 6 - 234
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-Components
#1: Protein | Mass: 24752.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4079 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HWU9 #2: Chemical | ChemComp-NAP / | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-NA / | #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: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, pH 5.6, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 41966 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 20.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WQM Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.653 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.647 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→50 Å
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Refine LS restraints |
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