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Yorodumi- PDB-5wqm: Crystal structure of a carbonyl reductase from Pseudomonas aerugi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wqm | ||||||
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Title | Crystal structure of a carbonyl reductase from Pseudomonas aeruginosa PAO1 (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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Li, S. / Wang, Y. / Bartlam, M. | ||||||
Funding support | China, 1items
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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 | 5wqm.cif.gz | 338.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wqm.ent.gz | 278.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/5wqm ftp://data.pdbj.org/pub/pdb/validation_reports/wq/5wqm | HTTPS FTP |
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-Related structure data
Related structure data | 5wqnC 5wqoC 5wqpC 3wxbS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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: 1 - 229
NCS ensembles :
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-Components
#1: Protein | Mass: 24340.660 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa 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 | #3: 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: 2.18 Å3/Da / Density % sol: 43.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 27161 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rpim(I) all: 0.03 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1291 / Rpim(I) all: 0.299 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WXB Resolution: 2.6→43.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 24.383 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.327
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.153 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→43.35 Å
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Refine LS restraints |
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