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- PDB-3hcg: Structure of the C-terminal domain (MsrB) of Neisseria meningitid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hcg | ||||||
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Title | Structure of the C-terminal domain (MsrB) of Neisseria meningitidis PilB (reduced form) | ||||||
![]() | Peptide methionine sulfoxide reductase msrA/msrB | ||||||
![]() | OXIDOREDUCTASE / PilB / Methionine sulfoxide reductase B / reduced form / Disulfide bond / Electron transport / Multifunctional enzyme / Redox-active center / Transport | ||||||
Function / homology | ![]() L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein modification process / response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ranaivoson, F.M. / Kauffmann, B. / Favier, F. | ||||||
![]() | ![]() Title: Methionine sulfoxide reductase B displays a high level of flexibility. Authors: Ranaivoson, F.M. / Neiers, F. / Kauffmann, B. / Boschi-Muller, S. / Branlant, G. / Favier, F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase B domain of Neisseria meningitidis PILB. Authors: Kauffmann, B. / Favier, F. / Olry, A. / Boschi-Muller, S. / Carpentier, P. / Branlant, G. / Aubry, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.8 KB | Display | ![]() |
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PDB format | ![]() | 115.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 466.5 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 16491.961 Da / Num. of mol.: 4 / Fragment: MsrB domain (UNP residues 377-522) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Z2491 / Gene: msrAB, NMA0290, pilB / Plasmid: pSKPILBMsrB / Production host: ![]() ![]() References: UniProt: Q9JWM8, peptide-methionine (R)-S-oxide reductase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0,5M KH2PO4, 0.1M TRIS HCl pH 8 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2001 | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.82→30 Å / Num. obs: 62578 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.045 / Net I/σ(I): 12.7 | ||||||||||||
Reflection shell | Resolution: 1.82→1.86 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.212 / % possible all: 91.8 |
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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 max: 60.44 Å2 / Biso mean: 24.031 Å2 / Biso min: 9.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→24.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Total num. of bins used: 20
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