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- PDB-2uwm: C-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 2uwm
TitleC-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX WITH SECIS RNA
Components
  • 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP *GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
  • SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
KeywordsTRANSLATION / 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 / RNA binding / cytosol
Similarity search - Function
: / Arc Repressor Mutant, subunit A - #2770 / Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Selenocysteine-specific elongation factor, beta-barrel domain / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific ...: / Arc Repressor Mutant, subunit A - #2770 / Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Selenocysteine-specific elongation factor, beta-barrel domain / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Small GTP-binding protein domain / Arc Repressor Mutant, subunit A / Translation protein, beta-barrel domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Selenocysteine-specific elongation factor
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsOse, T. / Soler, N. / Rasubala, L. / Kuroki, K. / Kohda, D. / Fourmy, D. / Yoshizawa, S. / Maenaka, K.
CitationJournal: 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
DepositionMar 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
B: SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
C: 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP *GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP *GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)74,1544
Polymers74,1544
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)160.074, 119.843, 50.461
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.86555, -0.04141, 0.49911), (0.01781, -0.9934, -0.1133), (0.5005, 0.10696, -0.8591)
Vector: -5.99753, 35.94452, 20.33857)

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Components

#1: Protein SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR / SELB TRANSLATION FACTOR


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 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP *GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3' / MRNA


Mass: 7386.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) MOORELLA THERMOACETICA (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN AND C TERMINAL RESIDUES MISSING BECAUSE OF THE POOR DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 66 %
Crystal growpH: 5.5
Details: MES PH5.5, PEG20K 18%, ETHYLENE GLYCOL 10%, NACL 0.1M, SPERMIDINE 20MM, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1
DetectorType: RIGAKU CCD / Detector: CCD / Date: Dec 16, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WSU

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3558 9 %RANDOM
Rwork0.2 ---
obs0.204 35981 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.74 Å2
2--0.33 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 976 0 292 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224422
X-RAY DIFFRACTIONr_bond_other_d0.0020.022772
X-RAY DIFFRACTIONr_angle_refined_deg1.4052.2476204
X-RAY DIFFRACTIONr_angle_other_deg0.92836718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20722.164171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59215578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9271541
X-RAY DIFFRACTIONr_chiral_restr0.0760.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_nbd_refined0.1890.2822
X-RAY DIFFRACTIONr_nbd_other0.2060.22862
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21978
X-RAY DIFFRACTIONr_nbtor_other0.0840.22037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.52563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88923163
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.44533197
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1354.53041
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 173
Rwork0.239 1939
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.7778-0.2747-0.74857.9368-2.24073.83430.0035-0.1051-1.09760.11550.09881.86750.4144-0.7735-0.1023-0.01390.00950.04540.1054-0.06130.4427-61.566-16.05917.7801
23.0233-1.6170.10091.79390.22590.97670.0230.0202-0.1302-0.0049-0.0041-0.11440.08490.1145-0.0189-0.0980.010.0239-0.09670.0016-0.1914-58.7089.52710.0136
35.63180.51731.41138.039-1.50029.1275-0.30530.82511.0249-1.0731-0.011.7826-0.4798-1.24030.31540.0951-0.0453-0.31280.29540.0330.3799-55.537550.8995-20.7385
41.74881.82990.92.87431.11251.4840.1192-0.1186-0.01080.1375-0.1263-0.2404-0.0779-0.00750.007-0.057-0.02690.0069-0.0410.0022-0.1613-52.185324.2944-16.6203
54.1163.6503-3.5833.2786-3.09553.2817-0.0758-0.07510.2187-0.03260.1124-0.0801-0.5949-0.0051-0.03660.0532-0.13580.0137-0.04870.02230.1449-52.537634.83784.8047
61.896-0.98062.56652.9239-3.0664.7773-0.09140.0237-0.087-0.05410.0896-0.02390.3396-0.01790.00180.03620.104-0.0074-0.06280.0238-0.0618-48.0893-0.5415-7.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A441 - 501
2X-RAY DIFFRACTION2A502 - 633
3X-RAY DIFFRACTION3B431 - 501
4X-RAY DIFFRACTION4B502 - 633
5X-RAY DIFFRACTION5C13 - 35
6X-RAY DIFFRACTION6D13 - 35

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