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- PDB-6y3g: Crystal structure of phenylalanine tRNA from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6y3g
TitleCrystal structure of phenylalanine tRNA from Escherichia coli
ComponentsRNA (75-MER)
KeywordsRNA / Transfer RNA with modifications
Function / homologyGUANIDINE / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBourgeois, G. / Mechulam, Y. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency14CE090021 France
CitationJournal: Rna / Year: 2020
Title: Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Authors: Bourgeois, G. / Seguin, J. / Babin, M. / Gondry, M. / Mechulam, Y. / Schmitt, E.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
F: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,23013
Polymers24,6211
Non-polymers60912
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-74 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)109.618, 109.618, 138.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: RNA chain RNA (75-MER)


Mass: 24620.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.95 Å3/Da / Density % sol: 75.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 12.4% PEG8000, 0.2M AcCa, 0.1M Hepes pH 7, 0.1M L-Pro

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Data collection

DiffractionMean temperature: 278 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 9432 / % possible obs: 99.7 % / Redundancy: 12.5 % / CC1/2: 0.99 / Net I/σ(I): 14.2
Reflection shellResolution: 3.1→3.3 Å / Num. unique obs: 1464 / CC1/2: 0.68 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDS1.17.1_3660data reduction
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCO

4yco


Resolution: 3.1→42.98 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5042
RfactorNum. reflection% reflection
Rfree0.2361 470 4.99 %
Rwork0.2153 --
obs0.2163 9420 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1609 29 2 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351813
X-RAY DIFFRACTIONf_angle_d0.85432816
X-RAY DIFFRACTIONf_chiral_restr0.0391368
X-RAY DIFFRACTIONf_plane_restr0.0055123
X-RAY DIFFRACTIONf_dihedral_angle_d20.7444921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.550.28711520.24152893X-RAY DIFFRACTION99.41
3.55-4.470.28641510.22692936X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.976895582 Å / Origin y: -39.6366701535 Å / Origin z: -7.70185779636 Å
111213212223313233
T0.653409213463 Å2-0.050592865553 Å2-0.0253364587083 Å2-1.16141788691 Å20.0486326213968 Å2--0.852577463238 Å2
L3.63371434084 °2-1.42839770114 °2-1.72822940764 °2-3.71327011844 °21.14285002437 °2--3.77333509331 °2
S-0.0459832748301 Å °0.543518186487 Å °0.379569422295 Å °-0.334087333319 Å °0.0219223194665 Å °-0.252067776587 Å °-0.658890007744 Å °0.257954723465 Å °0.0203208654306 Å °
Refinement TLS groupSelection details: all

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