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Yorodumi- PDB-2uwm: C-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uwm | ||||||
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Title | C-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX WITH SECIS RNA | ||||||
Components |
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Keywords | TRANSLATION / PROTEIN BIOSYNTHESIS / GTP-BINDING / NUCLEOTIDE- BINDING / SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR | ||||||
Function / homology | Function and homology information selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | MOORELLA THERMOACETICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Ose, T. / Soler, N. / Rasubala, L. / Kuroki, K. / Kohda, D. / Fourmy, D. / Yoshizawa, S. / Maenaka, K. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Structural Basis for Dynamic Interdomain Movement and RNA Recognition of the Selenocysteine-Specific Elongation Factor Selb. Authors: Ose, T. / Soler, N. / Rasubala, L. / Kuroki, K. / Kohda, D. / Fourmy, D. / Yoshizawa, S. / Maenaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uwm.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uwm.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 2uwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uwm ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uwm | HTTPS FTP |
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-Related structure data
Related structure data | 1wsuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.86555, -0.04141, 0.49911), Vector: |
-Components
#1: Protein | Mass: 29690.660 Da / Num. of mol.: 2 / Fragment: SECIS BINDING DOMAIN, RESIDUES 377-634 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q2RFK4 #2: RNA chain | Mass: 7386.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) MOORELLA THERMOACETICA (bacteria) #3: Water | ChemComp-HOH / | Sequence details | N AND C TERMINAL RESIDUES MISSING BECAUSE OF THE POOR DENSITY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 66 % |
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Crystal grow | pH: 5.5 Details: MES PH5.5, PEG20K 18%, ETHYLENE GLYCOL 10%, NACL 0.1M, SPERMIDINE 20MM, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Dec 16, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39541 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WSU Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.009 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 22.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→50 Å
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Refine LS restraints |
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