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- PDB-1lva: Crystal structure of a C-terminal fragment of Moorella thermoacet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lva | ||||||
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Title | Crystal structure of a C-terminal fragment of Moorella thermoacetica elongation factor SelB | ||||||
![]() | Selenocysteine-specific elongation factor | ||||||
![]() | TRANSLATION / winged-helix | ||||||
Function / homology | ![]() selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selmer, M. / Su, X.-D. | ||||||
![]() | ![]() Title: Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. Authors: Selmer, M. / Su, X.D. #1: ![]() Title: Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB Authors: Selmer, M. / Wilting, R. / Holmlund, D. / Su, X.-D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.9 KB | Display | ![]() |
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Full document | ![]() | 446.6 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.3 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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Unit cell |
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Components
#1: Protein | Mass: 29737.555 Da / Num. of mol.: 1 / Fragment: C-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.21 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, MES-Tris, yttrium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 298 K / pH: 8.6 Details: Selmer, M., (2002) Acta Crystallogr., Sect.D, 58, 1871. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 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: 2.12→20 Å / Num. all: 15941 / Num. obs: 15941 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.068 / Net I/σ(I): 28.2 | |||||||||||||||||||||
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1546 / Rsym value: 0.373 / % possible all: 99.9 | |||||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 100 % / Num. measured all: 138893 / Rmerge(I) obs: 0.068 | |||||||||||||||||||||
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.373 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 29.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.12→19.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.25 Å / Rfactor Rfree error: 0.013
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Refinement | *PLUS Lowest resolution: 19.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / Rfactor Rwork: 0.247 |