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- PDB-1l1d: Crystal structure of the C-terminal methionine sulfoxide reductas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l1d | ||||||
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Title | Crystal structure of the C-terminal methionine sulfoxide reductase domain (MsrB) of N. gonorrhoeae pilB | ||||||
![]() | peptide methionine sulfoxide reductase | ||||||
![]() | OXIDOREDUCTASE / cacodylate complex / cys-arg-asp catalytic triad / met-R(O) reductase / MsrB | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Lowther, W.T. / Weissbach, H. / Etienne, F. / Brot, N. / Matthews, B.W. | ||||||
![]() | ![]() Title: The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB. Authors: Lowther, W.T. / Weissbach, H. / Etienne, F. / Brot, N. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.9 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.8 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17020.541 Da / Num. of mol.: 2 / Fragment: MsrB domain, C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14930, EC: 1.8.4.13, L-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: 2.13 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris, cacodylate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Jul 21, 2001 | ||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→27.2 Å / Num. obs: 22584 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.3 | ||||||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.6 / % possible all: 89 | ||||||||||||
Reflection | *PLUS Num. measured all: 98562 / Rmerge(I) obs: 0.066 | ||||||||||||
Reflection shell | *PLUS % possible obs: 89.1 % / Rmerge(I) obs: 0.245 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE STRUCTURE FACTORS REPRESENT THE OPTIMIZED REFERENCE STRUCTURE FACTORS (FPSHA) AS DETERMINED BY SHARP. THE REFERENCE STRUCTURE FACTOR FOR A GIVEN REFLECTION IS DEFINED AS THE AVERAGE OF ...Details: THE STRUCTURE FACTORS REPRESENT THE OPTIMIZED REFERENCE STRUCTURE FACTORS (FPSHA) AS DETERMINED BY SHARP. THE REFERENCE STRUCTURE FACTOR FOR A GIVEN REFLECTION IS DEFINED AS THE AVERAGE OF THE STRUCTURE FACTORS FROM A THREE-WAVELENGTH MAD DATASET WHERE THE HEAVY-ATOM STRUCTURE FACTOR HAS BEEN SUBTRACTED.
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Displacement parameters | Biso mean: 20.7 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.236 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.2 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.207 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |