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- PDB-2aar: Structure of trigger factor binding domain in biologically homolo... -

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Basic information

Entry
Database: PDB / ID: 2aar
TitleStructure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L23
  • 50S ribosomal protein L29
  • Trigger Factor
KeywordsRIBOSOME / Trigger Factor / 50S / Cheperone / Tunnel
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 / protein transport / ribosome binding / cytosolic large ribosomal subunit / rRNA binding ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / cell cycle / cell division / cytoplasm
Similarity search - Function
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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein L23/L25, conserved site ...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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Trigger factor / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsBaram, D. / Pyetan, E. / Sittner, A. / Auerbach-Nevo, T. / Bashan, A. / Yonath, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action
Authors: Baram, D. / Pyetan, E. / Sittner, A. / Auerbach-Nevo, T. / Bashan, A. / Yonath, A.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
0: 23S ribosomal RNA
R: 50S ribosomal protein L23
W: 50S ribosomal protein L29
7: Trigger Factor


Theoretical massNumber of molelcules
Total (without water)964,3084
Polymers964,3084
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.386, 407.063, 692.746
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 / Coordinate model: Cα atoms only


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 L29 / Coordinate model: Cα atoms only


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


Mass: 12589.108 Da / Num. of mol.: 1 / Fragment: N-terminal Domain / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RT21

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 294915

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
CCP4model building
CNS1.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.5→8 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / Details: This entry contains C alpha only for the proteins.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 13451 5 %RANDOM
Rwork0.251 ---
all0.255 ---
obs0.267 270868 99 %-
Displacement parametersBiso mean: 98 Å2
Baniso -1Baniso -2Baniso -3
1--27.37 Å255.85 Å2-28.47 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.97 Å0.92 Å
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms271 59359 0 0 59630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.49

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