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- PDB-2fx3: Crystal Structure Determination of E. coli Elongation Factor, Tu ... -

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Basic information

Entry
Database: PDB / ID: 2fx3
TitleCrystal Structure Determination of E. coli Elongation Factor, Tu using a Twinned Data Set
ComponentsElongation factor TuEF-Tu
KeywordsTRANSLATION / EF-Tu / merohedral twinning
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Elongation factor Tu
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHeffron, S.E. / Moeller, R. / Jurnak, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Solving the structure of Escherichia coli elongation factor Tu using a twinned data set.
Authors: Heffron, S.E. / Moeller, R. / Jurnak, F.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6773
Polymers43,2091
Non-polymers4682
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.550, 69.550, 169.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Elongation factor Tu / EF-Tu / EF-Tu


Mass: 43209.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene: tufA / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q83JC4, UniProt: P0CE47*PLUS
#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.: 4 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.45 mM EF-Tu in 50 mM Tris, pH 7.8, 10 mM GDP, 10 mM magnesium chloride, 0.5% PEG 3350, 5.5 mM ammonium acetate, 2.7 mM ammonium citrate, 1.34 mM ChemDiv compound 1013-0135, VAPOR ...Details: 0.45 mM EF-Tu in 50 mM Tris, pH 7.8, 10 mM GDP, 10 mM magnesium chloride, 0.5% PEG 3350, 5.5 mM ammonium acetate, 2.7 mM ammonium citrate, 1.34 mM ChemDiv compound 1013-0135, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→60.232 Å / Num. obs: 6312 / % possible obs: 90.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Rsym value: 0.174 / Net I/σ(I): 3.2
Reflection shellResolution: 3.4→3.58 Å / % possible obs: 84.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / Num. measured all: 5800 / Num. unique obs: 844 / Rsym value: 0.48 / % possible all: 84.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D8T, chain A

1d8t


Resolution: 3.4→60.232 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used CNS specialized task files for refinement with hemihedrally twinned data. Twin operator was (-h,-k,l), and twin fraction was 0.294. R-factors reported are the twinned R-factors from CNS. ...Details: Used CNS specialized task files for refinement with hemihedrally twinned data. Twin operator was (-h,-k,l), and twin fraction was 0.294. R-factors reported are the twinned R-factors from CNS. (R-factors after detwinning: R-work=0.2867, R-free=0.3267)
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 586 8.4 %Used CNS task file make_cv_twin.inp to select cross-validation set such that pairs of twin-related reflections were designated to be in the same set, either the working set or the test set.
Rwork0.197 ---
all-6987 --
obs-6083 87.1 %-
Solvent computationBsol: 73.771 Å2
Displacement parametersBiso mean: 75.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.819 Å22.011 Å20 Å2
2--8.819 Å20 Å2
3----17.639 Å2
Refinement stepCycle: LAST / Resolution: 3.4→60.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 29 4 3014
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0114
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_dihedral_angle_d24.688
X-RAY DIFFRACTIONc_improper_angle_d1.184
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2MYTOPPAR:gdp_cns4.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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