+Open data
-Basic information
Entry | Database: PDB / ID: 7c2c | |||||||||
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Title | Esterase AlinE4 mutant, D162A | |||||||||
Components | SGNH-hydrolase family esterase | |||||||||
Keywords | HYDROLASE / esterase / SGNH-hydrolase family / marine | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Altererythrobacter indicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | |||||||||
Authors | Li, Z. / Li, J. | |||||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: C-terminal swapped dimers revealed a new catalytic mechanism of SGNH-hydrolase family esterases Authors: Li, Z. / Li, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c2c.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c2c.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 7c2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/7c2c ftp://data.pdbj.org/pub/pdb/validation_reports/c2/7c2c | HTTPS FTP |
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-Related structure data
Related structure data | 7c2aC 7c2dC 4jggS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20663.711 Da / Num. of mol.: 1 / Mutation: D162A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Altererythrobacter indicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH5, UniProt: A0A4P1LYH6*PLUS | ||||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 1M Sodium acetate, 100mM HEPES, pH 7.5, 50mM Cadmium sulfate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.06881 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06881 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→48.42 Å / Num. obs: 29038 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 12.39 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.71 |
Reflection shell | Resolution: 1.55→1.64 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 4174 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 4jgg Resolution: 1.55→48.42 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.7117
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→48.42 Å
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Refine LS restraints |
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LS refinement shell |
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