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Yorodumi- PDB-1lva: Crystal structure of a C-terminal fragment of Moorella thermoacet... -
+Open data
-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 | ||||||
Components | Selenocysteine-specific elongation factor | ||||||
Keywords | TRANSLATION / winged-helix | ||||||
Function / homology | Function and homology information selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Moorella thermoacetica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å | ||||||
Authors | Selmer, M. / Su, X.-D. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. Authors: Selmer, M. / Su, X.D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lva.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lva.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1lva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lva_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 1lva_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 1lva_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1lva_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lva ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lva | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Moorella thermoacetica (bacteria) / Gene: SelB(amino acids 370-634) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46455 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.7250, 0.7255, 0.9773, 0.9783, 0.9840, 0.9050 | |||||||||||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.12→19.24 Å / Isotropic thermal model: restrained / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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 |