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Yorodumi- PDB-2i4a: Crystal structure of thioredoxin from the acidophile Acetobacter aceti -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i4a | ||||||
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Title | Crystal structure of thioredoxin from the acidophile Acetobacter aceti | ||||||
Components | thioredoxin | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin / acidophile / disulfide exchange | ||||||
Function / homology | Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / BETA-MERCAPTOETHANOL Function and homology information | ||||||
Biological species | Acetobacter aceti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Starks, C.M. / Kappock, T.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti. Authors: Starks, C.M. / Francois, J.A. / Macarthur, K.M. / Heard, B.Z. / Kappock, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i4a.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i4a.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/2i4a ftp://data.pdbj.org/pub/pdb/validation_reports/i4/2i4a | HTTPS FTP |
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-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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Unit cell |
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Details | The biological unit is a monomer. There is one monomer in the asymmetric unit. |
-Components
#1: Protein | Mass: 11569.253 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Plasmid: pET-23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-BME / |
#3: 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: 1.97 Å3/Da / Density % sol: 37.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: microseeding in 100 mM sodium acetate (pH 4.6), 100 mM ammonium acetate, 24% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jul 15, 2006 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1→42.24 Å / Num. obs: 48392 / % possible obs: 96.2 % / Redundancy: 6.13 % / Biso Wilson estimate: 7.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3351 / Rsym value: 0.479 / % possible all: 67.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2trx Resolution: 1→35.2 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.588 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS USING MOLPROBITY
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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: 12.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1→35.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20
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