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Yorodumi- PDB-6kmo: Crystal structure of a novel esterase CinB from Enterobacter asburiae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmo | ||||||
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Title | Crystal structure of a novel esterase CinB from Enterobacter asburiae | ||||||
Components | Alpha/beta hydrolaseAlpha/beta hydrolase superfamily | ||||||
Keywords | HYDROLASE / Enterobacter asburiae / esterase / CinB | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter asburiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Shang, F. / Xu, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural and functional analyses of the lipase CinB from Enterobacter asburiae. Authors: Shang, F. / Lan, J. / Liu, W. / Chen, Y. / Wang, L. / Zhao, J. / Chen, J. / Gao, P. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kmo.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmo.ent.gz | 216.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmo ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36350.105 Da / Num. of mol.: 2 / Mutation: V9I,T23A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter asburiae (bacteria) / Gene: AN689_0218030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3AXI2 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.16 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate PH 5.6, 22% (w/v) Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979617 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979617 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 129477 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.79 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.125 |
Reflection shell | Resolution: 1.45→1.48 Å / Num. unique obs: 12496 / Rsym value: 0.224 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→36.69 Å / SU ML: 0.0882 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 12.7926
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→36.69 Å
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Refine LS restraints |
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LS refinement shell |
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