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- PDB-1lva: Crystal structure of a C-terminal fragment of Moorella thermoacet... -

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Basic information

Entry
Database: PDB / ID: 1lva
TitleCrystal structure of a C-terminal fragment of Moorella thermoacetica elongation factor SelB
ComponentsSelenocysteine-specific elongation factor
KeywordsTRANSLATION / winged-helix
Function / homology
Function and homology information


selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol
Similarity search - Function
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 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 / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 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
YTTRIUM ION / Selenocysteine-specific elongation factor
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsSelmer, 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
DepositionMay 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0114
Polymers29,7381
Non-polymers2743
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.841, 67.006, 105.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Selenocysteine-specific elongation factor / SelB translation factor / SelB


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
#2: Chemical ChemComp-Y1 / YTTRIUM ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
212 %PEG80001reservoir
30.1 MTris-HCl1reservoirpH8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.7250, 0.7255, 0.9773, 0.9783, 0.9840, 0.9050
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2001
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.7251
20.72551
30.97731
40.97831
50.9841
60.9051
ReflectionResolution: 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 shellResolution: 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

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→19.24 Å / Isotropic thermal model: restrained / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2755 -random
Rwork0.215 ---
all-29326 --
obs-28510 97.2 %-
Displacement parametersBiso mean: 29.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.12→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 7 108 2190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
LS refinement shellResolution: 2.12→2.25 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.271 434 -
Rwork0.239 --
obs-4550 93.1 %
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / Rfactor Rwork: 0.247

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