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Yorodumi- PDB-4grf: Crystal structure of thioredoxin domain of thiol-disulfide oxidor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4grf | ||||||
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Title | Crystal structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 (Target EFI-501010) from Bacteroides vulgatus | ||||||
Components | Putative thiol-disulfide oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN DOMAIN / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides vulgatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Imker, H.J. / Hammonds, J. / Al-Obaidi, N.F. / Stead, M. / Love, J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 from Bacteroides vulgatus Authors: Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Evans, B. / Chowdhury, S. / Hammonds, J. / Al- ...Authors: Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Evans, B. / Chowdhury, S. / Hammonds, J. / Al-Obaidi, N.F. / Stead, M. / Love, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4grf.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4grf.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 4grf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4grf ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4grf | HTTPS FTP |
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-Related structure data
Related structure data | 2lrnS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17364.656 Da / Num. of mol.: 1 / Fragment: thioredoxin domain RESIDUES 252-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2223 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L2G9 | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GSH / | #5: 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: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2M AMMONIUM SULFATE, 0.2M SODIUM CHLORIDE, 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→70 Å / Num. obs: 15565 / % possible obs: 99.6 % / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Biso Wilson estimate: 20.918 Å2 / Rsym value: 0.068 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2LRN Resolution: 1.76→44.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.185 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / 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: 28.535 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→44.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.761→1.807 Å / Total num. of bins used: 20
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