+Open data
-Basic information
Entry | Database: PDB / ID: 2vim | ||||||
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Title | X-ray structure of Fasciola hepatica thioredoxin | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN / TRX / THIOREDOXIN FOLD | ||||||
Function / homology | Function and homology information glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis Similarity search - Function | ||||||
Biological species | FASCIOLA HEPATICA (liver fluke) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Line, K. / Isupov, M.N. / Garcia-Rodriguez, E. / Maggioli, G. / Parra, F. / Littlechild, J.A. | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2008 Title: The Fasciola Hepatica Thioredoxin: High Resolution Structure Reveals Two Oxidation States. Authors: Line, K. / Isupov, M.N. / Garcia-Rodriguez, E. / Maggioli, G. / Parra, F. / Littlechild, J.A. #1: Journal: Parasitol.Res. / Year: 2001 Title: Heterologous Expression and Functional Characterisation of Thioredoxin from Fasciola Hepatica. Authors: Salazar-Calderon, M. / Martin-Alonso, J.M. / Ruiz De Eguino, A.D. / Parra, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vim.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vim.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vim ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vim | HTTPS FTP |
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-Related structure data
Related structure data | 2fa4S S: Starting model for refinement |
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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
#1: Protein | Mass: 11700.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9U1G7, phosphoadenylyl-sulfate reductase (thioredoxin) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 33.86 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 2 M AMMONIUM SULFATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL, NON DISPERSIVE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→38.69 Å / Num. obs: 16069 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 1.38→1.42 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 0.87 / % possible all: 56.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FA4 Resolution: 1.38→38.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.276 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACTIVE SITE CYSTEINE RESIDUES MODELLED IN BOTH REDUCED AND DISULFIDE OXIDATION STATES
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→38.69 Å
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Refine LS restraints |
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