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Yorodumi- PDB-2h6x: Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6x | ||||||
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Title | Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group | ||||||
Components | Thioredoxin | ||||||
Keywords | ELECTRON TRANSPORT / Alpha Beta | ||||||
Function / homology | Function and homology information DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gavira, J.A. / Godoy-Ruiz, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group Authors: Godoy-Ruiz, R. / Gavira, J.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations Authors: Godoy-Ruiz, R. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6x.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6x.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h6x_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 2h6x_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 2h6x_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2h6x_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6x ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6x | HTTPS FTP |
-Related structure data
Related structure data | 2trxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11687.388 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: peT30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2M889, UniProt: P0AA25*PLUS #2: Chemical | #3: 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: 2.79 Å3/Da / Density % sol: 55.95 % |
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Crystal grow | Temperature: 277 K / Method: counter-diffusion / pH: 3.5 Details: 60% (v/v) MPD, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 28, 2006 / Details: Montel Optics |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→51.36 Å / Num. all: 8147 / Num. obs: 8147 / % possible obs: 99.8 % / Redundancy: 7.28 % / Biso Wilson estimate: 51.288 Å2 / Rsym value: 0.0787 / Net I/σ(I): 9.08 |
Reflection shell | Resolution: 2.6→2.65 Å / Redundancy: 7.28 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 464 / Rsym value: 0.3161 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2TRX Resolution: 2.6→44.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.219 / SU B: 15.605 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.95 / ESU R Free: 0.36 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.014 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→44.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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