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Yorodumi- PDB-8h0d: Structure of the thermolabile hemolysin from Vibrio alginolyticus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h0d | ||||||
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Title | Structure of the thermolabile hemolysin from Vibrio alginolyticus (in complex with docosahexaenoic acid) | ||||||
Components | SGNH/GDSL hydrolase family protein | ||||||
Keywords | HYDROLASE / Vibrio / phospholipase / SGNH hydrolase / GDSL lipase / transferase / thermolabile hemolysin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio alginolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Ma, Q. / Wang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase. Authors: Wang, C. / Liu, C. / Zhu, X. / Peng, Q. / Ma, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h0d.cif.gz | 327.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h0d.ent.gz | 264.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/8h0d ftp://data.pdbj.org/pub/pdb/validation_reports/h0/8h0d | HTTPS FTP |
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-Related structure data
Related structure data | 8h09C 8h0aC 8h0bC 8h0cC 6jkzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48378.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: F0254_14065 / Plasmid: pETM13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A7Y4B3E8 #2: Chemical | ChemComp-HXA / | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | 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 Å3/Da / Density % sol: 38.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The crystal of ValTLH in complex with docosahexaenoic acid was grown in a drop containing 1.0 ul of protein solution (6 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300mM ...Details: The crystal of ValTLH in complex with docosahexaenoic acid was grown in a drop containing 1.0 ul of protein solution (6 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300mM NDSB201 with 1.25 mM docosahexaenoic acid) and 1.0 ul of reservoir solution (25% polyethylene glycol 20000, 0.15 M magnesium formate). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.008→81.779 Å / Num. obs: 51148 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Rsym value: 0.076 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.008→2.014 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 479 / CC1/2: 0.865 / Rpim(I) all: 0.365 / Rrim(I) all: 0.927 / Rsym value: 0.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JKZ Resolution: 2.01→81.779 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.161
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Displacement parameters | Biso max: 121.83 Å2 / Biso mean: 47.97 Å2 / Biso min: 23.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→81.779 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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