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- PDB-4zu9: Crystal structure of bacterial selenocysteine-specific elongation... -

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Basic information

Entry
Database: PDB / ID: 4zu9
TitleCrystal structure of bacterial selenocysteine-specific elongation factor EF-Sec
ComponentsElongation factor SelB
KeywordsTRANSLATION / Small GTPase / EF-Tu like
Function / homology
Function and homology information


selenocysteine incorporation / translational elongation / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / 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
Similarity search - Domain/homology
CYSTEINE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Elongation factor SelB
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.191 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB
Authors: Itoh, Y. / Sekine, S. / Yokoyama, S.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor SelB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6647
Polymers66,7081
Non-polymers9566
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-46 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.240, 114.240, 204.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Elongation factor SelB


Mass: 66707.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: selB / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O67141
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S

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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: 5 Å3/Da / Density % sol: 75.41 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 100 mM sodium acetate-HCl buffer, 1.7 M (NH4)2SO4, 20 mM L-cysteine, 3 mM GMPPNP, 10 mM Mg2SO4

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 42987 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.48 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 16.87
Reflection shellResolution: 3.19→3.38 Å / Redundancy: 15.46 % / Rmerge(I) obs: 0.02598 / Mean I/σ(I) obs: 1.26 / % possible all: 99.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
SHARPphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.191→40.39 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 27.42 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 2179 5.07 %Random selection
Rwork0.2065 ---
obs0.2091 42954 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.191→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 55 0 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014783
X-RAY DIFFRACTIONf_angle_d1.396423
X-RAY DIFFRACTIONf_dihedral_angle_d15.8991895
X-RAY DIFFRACTIONf_chiral_restr0.055739
X-RAY DIFFRACTIONf_plane_restr0.007798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1906-3.260.4131300.39512535X-RAY DIFFRACTION98
3.26-3.33580.31311440.34362523X-RAY DIFFRACTION100
3.3358-3.41910.30851430.30182531X-RAY DIFFRACTION100
3.4191-3.51150.38621670.26922547X-RAY DIFFRACTION100
3.5115-3.61480.31611350.26392556X-RAY DIFFRACTION100
3.6148-3.73140.33911500.25142517X-RAY DIFFRACTION100
3.7314-3.86470.28691490.23972553X-RAY DIFFRACTION100
3.8647-4.01930.33851470.21992546X-RAY DIFFRACTION100
4.0193-4.2020.25071230.20352592X-RAY DIFFRACTION100
4.202-4.42330.22581340.18182552X-RAY DIFFRACTION100
4.4233-4.70.20821340.16772520X-RAY DIFFRACTION100
4.7-5.06230.17641270.15742580X-RAY DIFFRACTION100
5.0623-5.57050.23611200.18572576X-RAY DIFFRACTION100
5.5705-6.37390.23651320.20972558X-RAY DIFFRACTION100
6.3739-8.02010.30581270.22042553X-RAY DIFFRACTION100
8.0201-40.39320.23771170.17722536X-RAY DIFFRACTION98
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)
15.87140.68714.27772.17710.21025.6123-0.28390.7928-0.1706-0.09090.4837-0.5593-0.3780.9061-0.18640.6396-0.02040.00740.8494-0.28420.734-28.845125.864728.3779
24.8258-3.42711.85462.1773-1.13011.5667-0.68090.16081.1770.6661-0.2694-0.3796-1.1675-0.67261.05491.81360.0918-0.8221.284-0.36441.8562-51.232153.733124.2203
35.6729-1.21440.3965.33971.12184.9564-0.3616-0.5753-0.18191.05070.57910.1937-0.0575-0.3432-0.14541.28060.21710.27220.65860.08650.6976-93.432158.55775.9116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 443 )
3X-RAY DIFFRACTION3chain 'A' and (resid 444 through 582 )

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