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Yorodumi- PDB-7e16: crystal structure of GDSL esterase from Geobacillus thermodenitri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+16 | ||||||
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Title | crystal structure of GDSL esterase from Geobacillus thermodenitrificans | ||||||
Components | GDSL-family esterase | ||||||
Keywords | HYDROLASE / esterase | ||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / GDSL-family esterase Function and homology information | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Chen, L. | ||||||
Citation | Journal: To Be Published Title: Rational engineering of substrate selectivity of GDSL esterase from Geobacillus thermodenitrificans Authors: Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e16.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e16.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 7e16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/7e16 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/7e16 | HTTPS FTP |
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-Related structure data
Related structure data | 1u8uS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29348.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2ZAB3 #2: 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: 3.1 Å3/Da / Density % sol: 60.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 22907 / % possible obs: 99.2 % / Redundancy: 20 % / CC1/2: 0.968 / Rpim(I) all: 0.024 / Rrim(I) all: 0.118 / Net I/σ(I): 1.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1126 / CC1/2: 0.933 / Rpim(I) all: 0.227 / Rsym value: 1.144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U8U Resolution: 2.62→32.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.094 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 200.27 Å2 / Biso mean: 70 Å2 / Biso min: 46.88 Å2
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Refinement step | Cycle: final / Resolution: 2.62→32.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.685 Å / Rfactor Rfree error: 0
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