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- PDB-2ywh: Crystal structure of GDP-bound LepA from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2ywh
TitleCrystal structure of GDP-bound LepA from Aquifex aeolicus
ComponentsGTP-binding protein LepA
KeywordsTRANSLATION / G domain / Beta-barrel / Ferredoxin-like domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / translation elongation factor activity / positive regulation of translation / ribosome binding / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Elongation factor 4, C-terminal domain / Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Elongation factor G C-terminus / Elongation factor EFG, domain V-like ...Elongation factor 4, C-terminal domain / Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Translation factors / EF-G domain III/V-like / Tr-type G domain, conserved site / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor 4
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKawazoe, M. / Takemoto, C. / Kaminishi, T. / Nishino, A. / Nakayama-Ushikoshi, R. / Hanawa-Suetsugu, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structures of GTP-binding protein LepA from Aquifex aeolicus.
Authors: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Nishino, A. / Nakayama-Ushikoshi, R. / Hanawa-Suetsugu, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: GTP-binding protein LepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2193
Polymers67,7511
Non-polymers4682
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.676, 116.118, 122.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTP-binding protein LepA


Mass: 67751.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1725 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67618
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris, 0.1M MgCl2, 20% w/v PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→45.18 Å / Num. obs: 28301 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.78 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 39.14
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.45 / Num. unique all: 2790 / Rsym value: 0.709 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YWE

2ywe


Resolution: 2.24→45.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2565419.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1453 5.1 %RANDOM
Rwork0.227 ---
obs0.227 28281 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6097 Å2 / ksol: 0.36949 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.75 Å20 Å20 Å2
2---7.65 Å20 Å2
3----7.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.24→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 29 112 4322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.39
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 246 5.4 %
Rwork0.314 4305 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gdp.paramgdp.top
X-RAY DIFFRACTION4ion.paramion.top

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