+Open data
-Basic information
Entry | Database: PDB / ID: 7yd2 | ||||||
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Title | SulE_P44R_S209A | ||||||
Components | Alpha/beta fold hydrolase | ||||||
Keywords | HYDROLASE / complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity Similarity search - Function | ||||||
Biological species | Hansschlegelia zhihuaiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Liu, B. / Ran, T. / Wang, W. / He, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity. Authors: Liu, B. / Wang, W. / Qiu, J. / Huang, X. / Qiu, S. / Bao, Y. / Xu, S. / Ruan, L. / Ran, T. / He, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yd2.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yd2.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yd2_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 7yd2_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 7yd2_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 7yd2_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/7yd2 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/7yd2 | HTTPS FTP |
-Related structure data
Related structure data | 7y0lSC 8golC 8goyC 8gp0C 8iveC 8ivmC 8ivnC 8ivsC 8ivtC 8iw3C 8iw6C 8j7gC 8j7jC 8j7kC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41219.379 Da / Num. of mol.: 2 / Mutation: P44R,S209A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hansschlegelia zhihuaiae (bacteria) / Gene: EK403_17710 / Production host: Escherichia coli (E. coli) References: UniProt: G9I933, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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-Non-polymers , 6 types, 684 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CIE / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→70.13 Å / Num. obs: 102138 / % possible obs: 98.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rpim(I) all: 0.031 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.61→1.65 Å / Num. unique obs: 7066 / CC1/2: 0.898 / Rpim(I) all: 0.192 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Y0L Resolution: 1.61→47.3 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 24.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→47.3 Å
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Refine LS restraints |
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