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Yorodumi- PDB-7xq3: Crystal structure of the tetramer of thioredoxin domain containin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xq3 | ||||||
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Title | Crystal structure of the tetramer of thioredoxin domain containing-protein of Oncomelania hupensis(OhTRP14) | ||||||
Components | Thioredoxin domain-containing protein 17 | ||||||
Keywords | ELECTRON TRANSPORT / Oncomelania hupensis / TRP14 / Redox regulation / Immunological properties | ||||||
Function / homology | Thioredoxin domain-containing protein 17-like / Thioredoxin domain-containing protein 17-like domain / Thioredoxin domain-containing protein 17-like, thioredoxin domain / protein-disulfide reductase (NAD(P)H) activity / Thioredoxin-like superfamily / Thioredoxin domain-containing protein 17 Function and homology information | ||||||
Biological species | Oncomelania hupensis (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Wang, S.Q. / Huang, S.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Fish Shellfish Immunol. / Year: 2022 Title: Structural insights into the redox regulation of Oncomelania hupensis TRP14 and its potential role in the snail host response to parasite invasion. Authors: Huang, S. / Wang, S. / Su, Z. / Cao, Y. / Hong, W. / Lin, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xq3.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xq3.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xq3 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xq3 | HTTPS FTP |
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-Related structure data
Related structure data | 7xpwC 1wouS 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
#1: Protein | Mass: 13874.693 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1CXZ6 #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: 2.24 Å3/Da / Density % sol: 44.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 30% PEG 3350, 0.2M Sodium malonate pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 47643 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 15.528 |
Reflection shell | Resolution: 1.77→1.8 Å / Rmerge(I) obs: 0.273 / Num. unique obs: 47643 / CC1/2: 0.967 / Rsym value: 0.273 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WOU Resolution: 1.77→35.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.355 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.181 / 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: 70.33 Å2 / Biso mean: 22.43 Å2 / Biso min: 8.09 Å2
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Refinement step | Cycle: final / Resolution: 1.77→35.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.815 Å / Rfactor Rfree error: 0
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