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Yorodumi- PDB-3e9j: Structure of the charge-transfer intermediate of the transmembran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e9j | ||||||
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Title | Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB | ||||||
Components |
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Keywords | OXIDOREDUCTASE / membrane protein complex / mechanism of disulfide bond formation / oxidative protein folding in Escherichia coli periplasm / X-ray crystal structure / charge transfer reaction intermediate / four helix bundle / Periplasm / Redox-active center / Cell inner membrane / Cell membrane / Chaperone / Electron transport / Membrane / Transmembrane / Transport | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / ubiquinone binding / cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / protein folding / outer membrane-bounded periplasmic space / response to heat / electron transfer activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Malojcic, G. / Owen, R.L. / Glockshuber, R. | ||||||
Citation | Journal: Febs Lett. / Year: 2008 Title: Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB. Authors: Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Glockshuber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e9j.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e9j.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 3e9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9j ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9j | HTTPS FTP |
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-Related structure data
Related structure data | 2hi7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 21122.959 Da / Num. of mol.: 2 / Mutation: C33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: BL21(DE3) / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: pDsbA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AEG4, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor #2: Protein | Mass: 20951.928 Da / Num. of mol.: 2 / Mutation: C8A, C49V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: HM125 / Gene: dsbB, roxB, ycgA, b1185, JW5182 / Plasmid: pDsbB / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 References: UniProt: P0A6M2, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor #3: Chemical | |
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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: 5.110001 Å3/Da / Density % sol: 75.929558 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 23% PEG550 MME, 50 mM Tris pH 8.9, 1.0 M ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→125 Å / Num. obs: 18142 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Rsym value: 0.072 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.7→3.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.436 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HI7 Resolution: 3.7→125.99 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.86 / SU B: 67.62 / SU ML: 0.953 / Cross valid method: THROUGHOUT / ESU R: 2.324 / ESU R Free: 0.79 / 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 mean: 160.416 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→125.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05
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LS refinement shell | Resolution: 3.7→3.796 Å / Total num. of bins used: 20
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