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- PDB-7bbn: Crystal structure of an ancient sequence-reconstructed Elongation... -

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Basic information

Entry
Database: PDB / ID: 7bbn
TitleCrystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317)
ComponentsElongation Factor TuEF-Tu
KeywordsTRANSLATION / Protein synthesis / Elongation Factor / ancestral sequence reconstruction / evolution
Function / homologyGUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMajumdar, S. / Bergfors, T. / Sanyal, S.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2018-05946 Sweden
Swedish Research Council2018-05498 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 317)
Authors: Majumdar, S. / Bergfors, T. / Sanyal, S.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation Factor Tu
B: Elongation Factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1856
Polymers86,2502
Non-polymers9354
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-38 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.342, 100.289, 160.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Elongation Factor Tu / EF-Tu


Mass: 43124.953 Da / Num. of mol.: 2
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 / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium citrate tribasic tetrathydrate, 20% w/v PEG 3350, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918401 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 1.68→29.44 Å / Num. obs: 88432 / % possible obs: 98.9 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.71100.8343772837870.7850.2680.8782.583.2
9.05-29.429.20.06258216320.9970.0210.06633.997.2

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 1.68→29.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.048 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 4447 5 %RANDOM
Rwork0.1912 ---
obs0.1927 83920 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 24.52 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 1.68→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 58 363 5951
Biso mean--17.4 30.99 -
Num. residues----727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135767
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175408
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6687858
X-RAY DIFFRACTIONr_angle_other_deg1.4581.57812532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5222.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4841537
X-RAY DIFFRACTIONr_chiral_restr0.0850.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
LS refinement shellResolution: 1.681→1.724 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.299 273 -
Rwork0.299 5500 -
obs--88.23 %

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