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Yorodumi- PDB-2vlv: Crystal structure of barley thioredoxin h isoform 2 in partially ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vlv | ||||||
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Title | Crystal structure of barley thioredoxin h isoform 2 in partially radiation-reduced state | ||||||
Components | THIOREDOXIN H ISOFORM 2. | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN DISULFIDE REDUCTASE / THIOREDOXIN-FOLD | ||||||
Function / homology | Function and homology information Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | HORDEUM VULGARE VAR. DISTICHUM (barley) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Maeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Crystal Structures of Barley Thioredoxin H Isoforms Hvtrxh1 and Hvtrxh2 Reveal Features Involved in Protein Recognition and Possibly in Discriminating the Isoform Specificity. Authors: Maeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vlv.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vlv.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vlv_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 2vlv_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 2vlv_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2vlv_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vlv ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vlv | HTTPS FTP |
-Related structure data
-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: 13179.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HORDEUM VULGARE VAR. DISTICHUM (barley) Variant: BARKE / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: Q7XZK2, thioredoxin-disulfide reductase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 38.21 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.3 Å / Num. obs: 21980 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / % possible all: 81.7 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.048 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 39.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→24.3 Å
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Refine LS restraints |
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