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- PDB-4pc7: Elongation factor Tu:Ts complex in a near GTP conformation. -

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Basic information

Entry
Database: PDB / ID: 4pc7
TitleElongation factor Tu:Ts complex in a near GTP conformation.
Components(Elongation factor ...) x 2
KeywordsTRANSLATION / G:GEF:Nucleotide complex / Elongation factor / Protein synthesis
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / zinc ion binding ...guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / : / Tetrahydropterin Synthase; Chain A ...Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / : / Tetrahydropterin Synthase; Chain A / Ubiquitin-associated (UBA) domain / 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 / UBA-like superfamily / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-PUL / Elongation factor Ts / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.6003 Å
AuthorsThirup, S.S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.
Authors: Thirup, S.S. / Van, L.B. / Nielsen, T.K. / Knudsen, C.R.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / exptl_crystal / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 1
C: Elongation factor Ts
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0595
Polymers73,6732
Non-polymers1,3863
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-41 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.820, 122.820, 173.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Elongation factor ... , 2 types, 2 molecules AC

#1: Protein Elongation factor Tu 1 / EF-Tu 1 / P-43


Mass: 43340.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47
#2: Protein Elongation factor Ts / EF-Ts


Mass: 30332.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsf, b0170, JW0165 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P1

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Non-polymers , 4 types, 4 molecules

#3: 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
#4: Chemical ChemComp-PUL / (1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOX ACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL 6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE / PULVOMYCIN


Mass: 839.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H66O13
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.12 Å3/Da / Density % sol: 75.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris, 1.8M (NH4)2SO4, 0.5mM GDPNP, 0.15mM pulvomycin, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.033 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.5→29.5 Å / Num. obs: 17862 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 10
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1702) / Classification: refinement
RefinementResolution: 3.6003→29.5 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 36.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 890 4.98 %random
Rwork0.2554 ---
obs0.2567 17857 99.26 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6003→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 93 1 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024961
X-RAY DIFFRACTIONf_angle_d0.5736701
X-RAY DIFFRACTIONf_dihedral_angle_d12.7011852
X-RAY DIFFRACTIONf_chiral_restr0.026776
X-RAY DIFFRACTIONf_plane_restr0.002869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6003-3.82540.4521460.40652777X-RAY DIFFRACTION100
3.8254-4.120.33581510.33412805X-RAY DIFFRACTION100
4.12-4.53330.31071470.2892818X-RAY DIFFRACTION100
4.5333-5.18620.25591490.25332833X-RAY DIFFRACTION100
5.1862-6.52240.30491480.27162838X-RAY DIFFRACTION100
6.5224-29.50140.21681490.17832896X-RAY DIFFRACTION97
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)
16.12881.40060.99574.06751.90594.8933-0.1482-0.09850.20150.00830.2043-0.1073-0.74660.2499-0.12610.6082-0.06350.08030.6170.1141.0791-21.682471.241358.0941
24.4501-0.13841.91571.3850.74043.4063-0.54170.93741.0962-0.1930.04460.1218-1.90040.83420.53271.8706-0.3197-0.27520.99890.3281.5742-16.438595.797348.581
37.26182.69571.20667.09322.4349.33830.2583-1.0393-2.23770.28130.252-1.1480.2666-0.5322-0.43150.83270.2456-0.12641.1189-0.04321.47751.861466.353774.7292
47.1555-3.0258-1.41952.45550.1247.7116-0.7778-0.08640.7655-0.41070.51790.3355-0.77330.18920.23661.4139-0.1859-0.2770.7186-0.11571.3617-0.505594.302390.0731
53.18930.223-0.2236.10341.74572.24630.25631.1603-0.2013-0.6917-0.2204-0.5651-0.54481.40750.01371.2629-0.1192-0.03311.84240.00541.339517.04184.303872.4258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 210 )
2X-RAY DIFFRACTION2chain 'A' and (resid 211 through 393 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 52 )
4X-RAY DIFFRACTION4chain 'C' and (resid 53 through 163 )
5X-RAY DIFFRACTION5chain 'C' and (resid 164 through 266 )

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