+Open data
-Basic information
Entry | Database: PDB / ID: 7c2a | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of AlinE4, a SGNH-hydrolase family esterase | |||||||||
Components | SGNH-hydrolase family esterase | |||||||||
Keywords | HYDROLASE / esterase / SGNH-hydrolase family / marine | |||||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / ACETATE ION / : / SGNH-hydrolase family esterase Function and homology information | |||||||||
Biological species | Altererythrobacter indicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å | |||||||||
Authors | Li, Z. / Li, J. | |||||||||
Funding support | China, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7c2a.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7c2a.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 7c2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c2a_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7c2a_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 7c2a_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7c2a_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/7c2a ftp://data.pdbj.org/pub/pdb/validation_reports/c2/7c2a | HTTPS FTP |
-Related structure data
Related structure data | 7c2cC 7c2dC 4jggS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20707.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Altererythrobacter indicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH5 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→48.46 Å / Num. obs: 64618 / % possible obs: 99.03 % / Redundancy: 2 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.18→1.21 Å / Rmerge(I) obs: 0.645 / Num. unique obs: 4370 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: 4jgg Resolution: 1.18→48.46 Å / SU ML: 0.0774 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5187
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→48.46 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|