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- PDB-6i8r: Crystal structure of an ancient sequence-reconstructed Elongation... -

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Basic information

Entry
Database: PDB / ID: 6i8r
TitleCrystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170)
ComponentsElongation Factor Tu
KeywordsTRANSLATION / Protein Synthesis / Elongation Factor / Sequence reconstruction / ancient protein
Function / homologyTranslation factors / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMajumdar, S. / Bergfors, T. / Sanyal, S.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2014-4423 Sweden
Swedish Research Council2016-06264 Sweden
Wenner-Gren FoundationUPD 2017-0238 Sweden
Knut and Alice Wallenberg FoundationKAW 2017.0055 Sweden
CitationJournal: To be published
Title: Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170)
Authors: Majumdar, S. / Bergfors, T. / Sanyal, S.
History
DepositionNov 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,3383
Polymers43,8711
Non-polymers4682
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-16 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.225, 73.956, 115.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elongation Factor Tu


Mass: 43870.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium Chloride, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2→45.42 Å / Num. obs: 33564 / % possible obs: 99 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 17.5 / Num. measured all: 325593
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.059.61.59623910.7240.5341.68696.5
8.93-45.4280.0314470.9990.0120.03398

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DG1

1dg1


Resolution: 2→45.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.351 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1723 5.1 %RANDOM
Rwork0.1923 ---
obs0.1949 31782 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 263.76 Å2 / Biso mean: 66.933 Å2 / Biso min: 43 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å20 Å20 Å2
2--9.19 Å2-0 Å2
3----5.41 Å2
Refinement stepCycle: final / Resolution: 2→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 29 242 3071
Biso mean--64.49 82.68 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192879
X-RAY DIFFRACTIONr_bond_other_d0.0020.022771
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9833910
X-RAY DIFFRACTIONr_angle_other_deg1.12236379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6615363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27823.984123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3941521
X-RAY DIFFRACTIONr_chiral_restr0.1140.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213211
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02604
LS refinement shellResolution: 1.997→2.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 111 -
Rwork0.418 2271 -
all-2382 -
obs--96.28 %

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