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

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Basic information

Entry
Database: PDB / ID: 6gfu
TitleCrystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262)
ComponentsElongation Factor TuEF-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. / Tarafder, A.D. / Ge, X. / Kacar, B. / 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 262)
Authors: Majumdar, S. / Tarafder, A.D. / Ge, X. / Kacar, B. / Sanyal, S.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)44,5773
Polymers44,1091
Non-polymers4682
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-17 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.944, 73.691, 113.756
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 / EF-Tu


Mass: 44109.219 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 / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol 0.03M of each ethylene glycol (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol), 0.1M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2→61.85 Å / Num. obs: 33001 / % possible obs: 99.1 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Net I/σ(I): 13.9
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
2-2.059.61.0522230223180.8130.3511.1112.596
8.92-45.0690.06240544490.9980.0210.06536.499.6

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Processing

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

1efc


Resolution: 2→61.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.288 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1674 5.1 %RANDOM
Rwork0.1786 ---
obs0.1815 31282 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.91 Å2 / Biso mean: 35.594 Å2 / Biso min: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--3.52 Å2-0 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 2→61.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 29 136 3081
Biso mean--28.33 41.64 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192997
X-RAY DIFFRACTIONr_bond_other_d0.0020.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9854073
X-RAY DIFFRACTIONr_angle_other_deg1.03136651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79124.309123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6361519
X-RAY DIFFRACTIONr_chiral_restr0.1190.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
LS refinement shellResolution: 1.995→2.047 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 122 -
Rwork0.269 2189 -
all-2311 -
obs--95.5 %

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