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- PDB-6eze: The open conformation of E.coli Elongation Factor Tu in complex w... -

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Basic information

Entry
Database: PDB / ID: 6eze
TitleThe open conformation of E.coli Elongation Factor Tu in complex with GDPNP.
ComponentsElongation factor Tu 2EF-Tu
KeywordsTRANSLATION / Elongation Factor G-protein
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / DI(HYDROXYETHYL)ETHER / Elongation factor Tu 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsJohansen, J.S. / Blaise, M. / Thirup, S.S.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form.
Authors: Johansen, J.S. / Kavaliauskas, D. / Pfeil, S.H. / Blaise, M. / Cooperman, B.S. / Goldman, Y.E. / Thirup, S.S. / Knudsen, C.R.
History
DepositionNov 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 2
B: Elongation factor Tu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,18120
Polymers86,7412
Non-polymers2,44018
Water4,630257
1
A: Elongation factor Tu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,70411
Polymers43,3701
Non-polymers1,33310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor Tu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4779
Polymers43,3701
Non-polymers1,1078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.243, 243.589, 67.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Elongation factor Tu 2 / EF-Tu / EF-Tu 2 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 43370.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / References: UniProt: P0CE48

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Non-polymers , 6 types, 275 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein konc. 8 mg/ml in 30 mM KCl, 20mM Hepes pH 7.5,5mM MgCl2, 1mM DTT 1 ul protein sample mixed with 1ul reservoir. Reservoir: 2M Ammonium sulfate 100 mM Hepes pH 7.5 2% (v/v) PEG 400 1mM ...Details: Protein konc. 8 mg/ml in 30 mM KCl, 20mM Hepes pH 7.5,5mM MgCl2, 1mM DTT 1 ul protein sample mixed with 1ul reservoir. Reservoir: 2M Ammonium sulfate 100 mM Hepes pH 7.5 2% (v/v) PEG 400 1mM DTT and streak seeded.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.47→29.7 Å / Num. obs: 36491 / % possible obs: 98.3 % / Redundancy: 7.8 % / Biso Wilson estimate: 34.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Net I/σ(I): 18.1
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 7 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3509 / CC1/2: 0.799 / % possible all: 95.64

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 2.47→29.697 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.2118 2069 5.68 %
Rwork0.172 --
obs0.1742 36410 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→29.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 149 257 6348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026189
X-RAY DIFFRACTIONf_angle_d0.598380
X-RAY DIFFRACTIONf_dihedral_angle_d9.0783699
X-RAY DIFFRACTIONf_chiral_restr0.045948
X-RAY DIFFRACTIONf_plane_restr0.0041074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.52750.33071310.31112173X-RAY DIFFRACTION95
2.5275-2.59060.32481360.25052270X-RAY DIFFRACTION98
2.5906-2.66060.25651330.21672202X-RAY DIFFRACTION98
2.6606-2.73890.24141380.19482282X-RAY DIFFRACTION100
2.7389-2.82720.26951340.18942235X-RAY DIFFRACTION98
2.8272-2.92820.25931380.19552287X-RAY DIFFRACTION98
2.9282-3.04530.27131370.2072261X-RAY DIFFRACTION99
3.0453-3.18370.22761360.17692274X-RAY DIFFRACTION99
3.1837-3.35140.21621390.17332302X-RAY DIFFRACTION99
3.3514-3.5610.22141380.16592280X-RAY DIFFRACTION99
3.561-3.83550.17011370.15992295X-RAY DIFFRACTION98
3.8355-4.22050.18171410.14592314X-RAY DIFFRACTION99
4.2205-4.82890.15131410.11892346X-RAY DIFFRACTION99
4.8289-6.07530.1831430.15242387X-RAY DIFFRACTION99
6.0753-29.69940.19911470.1732433X-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)
13.3083-0.16620.3543.7717-0.10322.2856-0.096-0.0384-0.0517-0.01790.02840.1910.0265-0.1410.06910.1617-0.0004-0.00140.185-0.00820.146935.327740.3282-15.9735
24.8405-0.47212.0524.3726-0.42977.00720.24090.30830.173-0.4066-0.16350.4775-0.1986-0.2625-0.06350.2330.06270.00830.1860.01040.250317.087157.2209-0.3497
33.2748-1.010.47793.0589-0.66172.05650.07120.3386-0.3163-0.1326-0.06640.13020.11980.1470.00670.21450.00960.00550.2026-0.04940.251.444318.9674-11.0275
42.28391.27790.50043.80241.09870.49320.061-0.52050.13910.6266-0.26870.45120.1801-0.1960.16940.4287-0.08310.09320.3528-0.04140.2928.209133.169424.8704
54.0583-1.3845-1.14986.21820.54065.0669-0.0224-0.1275-0.36820.4370.0436-0.44450.55780.5087-0.02770.34910.0467-0.0920.23860.03060.369720.519313.022811.0179
63.0399-0.1527-0.98042.2133-0.98043.4563-0.1016-0.46990.03340.26750.0784-0.1160.14620.25910.02650.2823-0.0136-0.02680.2693-0.01770.162829.287346.775121.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 300 through 393 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 198 )
4X-RAY DIFFRACTION4chain 'B' and (resid 199 through 299)
5X-RAY DIFFRACTION5chain 'B' and (resid 300 through 393 )
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 299 )

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