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Yorodumi- PDB-2iwt: Thioredoxin h2 (HvTrxh2) in a mixed disulfide complex with the ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iwt | ||||||
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Title | Thioredoxin h2 (HvTrxh2) in a mixed disulfide complex with the target protein BASI | ||||||
Components |
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Keywords | OXIDOREDUCTASE / PROTEASE INHIBITOR / DISULFIDE REDUCTASE / BASI / AMY2 / REDOX / THIOREDOXIN / SUBSTRATE RECOGNITION / DISULFIDE INTERMEDIATE / ALPHA-AMYLASE INHIBITOR / SERINE PROTEASE INHIBITOR | ||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / serine-type endopeptidase inhibitor activity Similarity search - Function | ||||||
Biological species | HORDEUM VULGARE (barley) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Maeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural Basis for Target Protein Recognition by the Protein Disulfide Reductase Thioredoxin. Authors: Maeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A. #1: Journal: Proteomics / Year: 2005 Title: Identification of Thioredoxin H-Reducible Disulphides in Proteomes by Differential Labelling of Cysteines: Insight Into Recognition and Regulation of Proteins in Barley Seeds by Thioredoxin H Authors: Maeda, K. / Finnie, C. / Svensson, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iwt.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iwt.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 2iwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iwt_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 2iwt_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 2iwt_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2iwt_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iwt ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iwt | HTTPS FTP |
-Related structure data
Related structure data | 1avaS 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: 13445.537 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DISULFIDE LINK BETWEEN MOL A C46 AND MOL B C148 / Source: (gene. exp.) HORDEUM VULGARE (barley) / Variant: BARKE / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q7XZK2 | ||||||||
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#2: Protein | Mass: 20923.406 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DISULFIDE LINK BETWEEN MOL A C46 AND MOL B C148 / Source: (gene. exp.) HORDEUM VULGARE (barley) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P07596 | ||||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Has protein modification | Y | Sequence details | N-TERMINAL SEQUENCE DISCREPANCIES IN BOTH MOLECULES ARE THE RESULT OF SEQUENCE MODIFICATIONS ...N-TERMINAL SEQUENCE DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | pH: 5 / Details: 0.1 M CITRIC ACID PH 5.0, 12% PEG6000 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 7, 2006 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→65.65 Å / Num. obs: 16933 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AVA AND UNPUBLISHED STRUCTURE OF BARLEY TRXH2 Resolution: 2.3→24.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1634340.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.7789 Å2 / ksol: 0.306568 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→24.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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