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- PDB-2d3o: Structure of Ribosome Binding Domain of the Trigger Factor on the... -

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Basic information

Entry
Database: PDB / ID: 2d3o
TitleStructure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans
Components
  • 23S RIBOSOMAL RNA
  • 50S RIBOSOMAL PROTEIN L23
  • 50S RIBOSOMAL PROTEIN L24
  • 50S RIBOSOMAL PROTEIN L29
  • Trigger Factor
KeywordsRIBOSOME / Trigger Factor / Nascent Chain / 50S / Protein Folding / SRP
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal large subunit assembly / ribosome binding / protein transport / cytosolic large ribosomal subunit ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal large subunit assembly / ribosome binding / protein transport / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / cell cycle / translation / cell division / cytoplasm
Similarity search - Function
Trigger factor ribosome-binding domain / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Helix Hairpins - #310 ...Trigger factor ribosome-binding domain / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Helix Hairpins - #310 / Peptidyl-prolyl cis-trans isomerase domain superfamily / RRM (RNA recognition motif) domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L24 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Helix Hairpins / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Trigger factor / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.35 Å
AuthorsSchluenzen, F. / Wilson, D.N. / Hansen, H.A. / Tian, P. / Harms, J.M. / McInnes, S.J. / Albrecht, R. / Buerger, J. / Wilbanks, S.M. / Fucini, P.
CitationJournal: Structure / Year: 2005
Title: The Binding Mode of the Trigger Factor on the Ribosome: Implications for Protein Folding and SRP Interaction
Authors: Schlunzen, F. / Wilson, D.N. / Tian, P. / Harms, J.M. / McInnes, S.J. / Hansen, H.A. / Albrecht, R. / Buerger, J. / Wilbanks, S.M. / Fucini, P.
History
DepositionSep 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Database references / Category: struct_ref / Item: _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RIBOSOMAL RNA
R: 50S RIBOSOMAL PROTEIN L23
S: 50S RIBOSOMAL PROTEIN L24
W: 50S RIBOSOMAL PROTEIN L29
1: Trigger Factor


Theoretical massNumber of molelcules
Total (without water)976,5965
Polymers976,5965
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.500, 410.500, 695.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 6460405
#2: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK0
#3: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ1
#4: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ4
#5: Protein Trigger Factor / TF


Mass: 12492.059 Da / Num. of mol.: 1 / Fragment: Ribosome Binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9RT21

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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 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5HEPES11
6NH4CL11
7MGCL212
8KCL12
9HEPES12
10NH4CL12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 13, 2004
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.35→30 Å / Num. all: 344768 / Num. obs: 322358 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.4 Å2
Reflection shellResolution: 3.35→3.47 Å / % possible all: 75.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.35→29.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 24577187.52 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME
RfactorNum. reflection% reflectionSelection details
Rfree0.322 14389 4.5 %RANDOM
Rwork0.299 ---
all0.299 344768 --
obs0.299 322358 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 1.19822 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1--29.15 Å20 Å20 Å2
2--49.05 Å20 Å2
3----19.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.72 Å0.59 Å
Luzzati d res low-7 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.35→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 60132 0 0 63004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d1.73
LS refinement shellResolution: 3.35→3.47 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.335 25804 -
obs--75.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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