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- PDB-6y4b: Structure of cyclodipeptide synthase from Candidatus Glomeribacte... -

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Basic information

Entry
Database: PDB / ID: 6y4b
TitleStructure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe
Components
  • Cyclodipeptide synthase
  • RNA (77-MER)
KeywordsRNA BINDING PROTEIN / cyclodipeptide synthase / tRNA / Complex
Function / homologyCyclodipeptide synthase superfamily / aminoacyltransferase activity / PHENYLALANINE / RNA / RNA (> 10) / Cyclodipeptide synthase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Candidatus Glomeribacter gigasporarum BEG34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 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 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: 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
F: RNA (77-MER)
A: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8043
Polymers58,6392
Non-polymers1651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-20 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.834, 254.834, 69.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#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+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: RNA chain RNA (77-MER)


Mass: 24519.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNA is aminoacylated, adenosine 76 is bounded to phenylalanine
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein Cyclodipeptide synthase


Mass: 34119.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Glomeribacter gigasporarum BEG34 (bacteria)
Gene: CAGGBEG34_30028 / Production host: Escherichia coli (E. coli) / References: UniProt: G2JBB2
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
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: 5.55 Å3/Da / Density % sol: 77.84 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 10% PEG8000, 0.17 M AcCa, 0.17 M Guanidinium hydrochloride, 0.1 M Hepes pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 5→50 Å / Num. obs: 6120 / % possible obs: 95.6 % / Redundancy: 33.2 % / Biso Wilson estimate: 214.56 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7
Reflection shellResolution: 5→5.3 Å / Redundancy: 32 % / Mean I/σ(I) obs: 1 / Num. unique obs: 867 / CC1/2: 0.58 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS1.17.1_3660data reduction
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLP

5mlp


Resolution: 5→48.16 Å / SU ML: 1.0625 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3158 215 4.98 %
Rwork0.304 4100 -
obs0.3047 4315 70.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 139.07 Å2
Refinement stepCycle: LAST / Resolution: 5→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 1634 0 0 2968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223164
X-RAY DIFFRACTIONf_angle_d0.64594700
X-RAY DIFFRACTIONf_chiral_restr0.0318619
X-RAY DIFFRACTIONf_plane_restr0.0038386
X-RAY DIFFRACTIONf_dihedral_angle_d20.25971241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5-6.30.5531710.45921162X-RAY DIFFRACTION41.49
6.3-48.160.28051440.28262938X-RAY DIFFRACTION98.34
Refinement TLS params.Method: refined / Origin x: -80.2336000483 Å / Origin y: 69.1408391067 Å / Origin z: 3.14746588878 Å
111213212223313233
T0.239901044783 Å2-0.541033478684 Å20.0675871126923 Å2-1.30573308465 Å2-0.750519766849 Å2--0.984832427339 Å2
L5.41545539992 °20.68715505611 °20.129769128946 °2-2.15138614768 °2-0.269086836002 °2--1.24257125473 °2
S0.0865425523863 Å °-1.70979102773 Å °-0.0666863934079 Å °0.450778012993 Å °-0.0259031522297 Å °0.663453660244 Å °-0.327969720799 Å °-0.968640668265 Å °-0.0109763117182 Å °
Refinement TLS groupSelection details: all

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