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Open data
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Basic information
Entry | Database: PDB / ID: 3dvx | ||||||
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Title | Crystal structure of reduced DsbA3 from Neisseria meningitidis | ||||||
![]() | Thiol:disulfide interchange protein DsbA | ||||||
![]() | OXIDOREDUCTASE / thiol-oxidoreductase / neisseria / DsbA / disulfide bond | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lafaye, C. / Serre, L. | ||||||
![]() | ![]() Title: Biochemical and structural study of the homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis. Authors: Lafaye, C. / Iwema, T. / Carpentier, P. / Jullian-Binard, C. / Kroll, J.S. / Collet, J.F. / Serre, L. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Preliminary crystallographic data of the three homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis. Authors: Lafaye, C. / Iwema, T. / Ferrer, J.L. / Kroll, J.S. / Griat, M. / Serre, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.9 KB | Display | ![]() |
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PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 459.8 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dvwSC ![]() 3hz8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22233.057 Da / Num. of mol.: 2 / Fragment: Mature form: UNP residues 20-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Details: 2.2 M Ammonium sulfate, 0.25 M Sodium malonate, 0.1 M MES pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 12602 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.099 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.272 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DVW Resolution: 2.8→19.79 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.861 / SU B: 16.744 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / 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: 31.545 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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