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Open data
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Basic information
Entry | Database: PDB / ID: 3dvw | ||||||
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Title | Crystal structure of reduced DsbA1 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 | ![]() | 53.8 KB | Display | ![]() |
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PDB format | ![]() | 38.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21510.436 Da / Num. of mol.: 1 / Fragment: Truncated mature form: UNP residues 41-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.4 M Ammonium sulfate, 0.1 M Bicine pH 9.0 or 1.6 M Trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD Details: Mirrors, horizontal focusing by sagitally curved 2nd crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46 Å / Num. obs: 26907 / % possible obs: 99.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.241 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 12.808 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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