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- PDB-5opd: Structure of phosphorylated EF-Tu in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5opd
TitleStructure of phosphorylated EF-Tu in complex with GTP
ComponentsElongation factor Tu 1EF-Tu
KeywordsTRANSLATION / protein-nucelotide complex
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / GTPase activity / GTP binding / 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'-TRIPHOSPHATE / IODIDE ION / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli O9:H4
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsGarcia-Pino, A.
CitationJournal: To Be Published
Title: Structure of phosphorylated EF-Tu in complex with GTP
Authors: Garcia-Pino, A.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,35440
Polymers88,4992
Non-polymers4,85538
Water5,621312
1
A: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71220
Polymers44,2491
Non-polymers2,46219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,64220
Polymers44,2491
Non-polymers2,39319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.840, 61.880, 65.480
Angle α, β, γ (deg.)70.37, 75.83, 89.41
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 44249.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O9:H4 (strain HS) (bacteria)
Gene: tuf1, EcHS_A3535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8A5E6

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Non-polymers , 6 types, 350 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3550, 0.1 M Bis-Tris propane pH 6.5 and 0.2 M Sodium Iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.8369 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8369 Å / Relative weight: 1
ReflectionResolution: 2.75→51.37 Å / Num. obs: 20752 / % possible obs: 96.6 % / Redundancy: 6 % / Biso Wilson estimate: 40.67 Å2 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→51.37 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.813 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.258 978 4.71 %RANDOM
Rwork0.181 ---
obs0.185 20752 93.4 %-
Displacement parametersBiso mean: 18.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.5389 Å2-0.3609 Å2-0.7291 Å2
2---1.4631 Å2-0.4334 Å2
3----0.0758 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.75→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 127 312 6070
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.247931HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1965SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes885HARMONIC5
X-RAY DIFFRACTIONt_it5828HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion20.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion796SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6641SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2987 142 6.06 %
Rwork0.2086 2200 -
all0.2141 2342 -
obs--72.49 %
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)
10.4440.3415-0.44620.8905-0.38860.7048-0.0424-0.0363-0.0024-0.0141-0.0724-0.0038-0.0481-0.06010.1148-0.0337-0.0095-0.0259-0.07160.0223-0.005815.988322.030359.291
20.454-0.0040.1571.2124-0.50610.24330.0432-0.0280.0221-0.0101-0.03460.0227-0.0450.0102-0.00860.0426-0.03970.0154-0.0929-0.0222-0.068436.83934.243240.0161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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