+Open data
-Basic information
Entry | Database: PDB / ID: 3dks | |||||||||
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Title | DsbA substrate complex | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / DSBA / MIXED DISULFIDE / Redox-active center / Protease | |||||||||
Function / homology | Function and homology information protein-disulfide reductase activity / cell redox homeostasis / periplasmic space Similarity search - Function | |||||||||
Biological species | Shigella flexneri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Paxman, J.J. / Borg, N.A. / Horne, J. / Rossjohn, J. / Thompson, P.E. / Piek, S. / Kahler, C.M. / Sakellaris, H. / Scanlon, M.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The structure of the bacterial oxidoreductase enzyme DsbA in complex with a peptide reveals a basis for substrate specificity in the catalytic cycle of DsbA enzymes Authors: Paxman, J.J. / Borg, N.A. / Horne, J. / Thompson, P.E. / Chin, Y. / Sharma, P. / Simpson, J.S. / Wielens, J. / Piek, S. / Kahler, C.M. / Sakellaris, H. / Pearce, M. / Bottomley, S.P. / ...Authors: Paxman, J.J. / Borg, N.A. / Horne, J. / Thompson, P.E. / Chin, Y. / Sharma, P. / Simpson, J.S. / Wielens, J. / Piek, S. / Kahler, C.M. / Sakellaris, H. / Pearce, M. / Bottomley, S.P. / Rossjohn, J. / Scanlon, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dks.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dks.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 3dks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dks ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dks | HTTPS FTP |
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-Related structure data
Related structure data | 1dsbS 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: 21154.959 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: dsbA, SF3931, S3816 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus References: UniProt: P52235, protein-disulfide reductase (glutathione) #2: Protein/peptide | Mass: 1085.272 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthesised N-terminally acetylated peptide from the autotransporter protein siga #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: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.2M AMMONIUM ACETATE, 20%(W/V) PEG 4000, 0.1M sodium citrate(pH 5.8), pH 6.700000, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→69.34 Å / Num. obs: 67234 / Redundancy: 7.1 % / Net I/σ(I): 15.8 |
Reflection shell | Highest resolution: 1.9 Å / Redundancy: 6.6 % / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DSB Resolution: 1.9→69.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.694 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.15 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.54 Å2 / Biso mean: 24.837 Å2 / Biso min: 3.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→69.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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