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Yorodumi- PDB-2h6y: Crystal Structure of Thioredoxin Mutant E48D in Hexagonal (p61) S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6y | ||||||
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Title | Crystal Structure of Thioredoxin Mutant E48D 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 Mutant E48D 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, R. / Sanchez-Ruiz, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6y.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6y.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6y ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6y | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 11673.361 Da / Num. of mol.: 2 / Mutation: E48D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / 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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 277 K / Method: counter-diffusion / pH: 3.5 Details: 60% (v/v) MPD, AcNa 15 mM pH 3.5, 1 mM Ac2Cu, Counter-diffusion, 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: Dec 20, 2005 / 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: 2.4→50.8 Å / Num. all: 9093 / Num. obs: 9093 / % possible obs: 99.5 % / Redundancy: 10.25 % / Biso Wilson estimate: 35.742 Å2 / Rsym value: 0.048 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.45 / Num. unique all: 492 / Rsym value: 0.3529 / % possible all: 93.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2TRX_A Resolution: 2.4→50.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.174 / SU B: 15.511 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.267 / 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50.8 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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Refinement TLS params. | Method: refined / Origin x: -4.134 Å / Origin y: 37.109 Å / Origin z: 18.29 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 2 - 108 / Label seq-ID: 2 - 108
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