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- PDB-2dyj: Crystal structure of ribosome-binding factor A from Thermus therm... -

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Basic information

Entry
Database: PDB / ID: 2dyj
TitleCrystal structure of ribosome-binding factor A from Thermus thermophilus HB8
ComponentsRibosome-binding factor A
KeywordsRIBOSOMAL PROTEIN / 16S rRNA processing / 17S RNA / KH domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


maturation of SSU-rRNA / rRNA binding / cytoplasm
Similarity search - Function
Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding factor A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKawazoe, M. / Takemoto, C. / Nakayama-Ushikoshi, R. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Mol Cell / Year: 2007
Title: Structural aspects of RbfA action during small ribosomal subunit assembly.
Authors: Partha P Datta / Daniel N Wilson / Masahito Kawazoe / Neil K Swami / Tatsuya Kaminishi / Manjuli R Sharma / Timothy M Booth / Chie Takemoto / Paola Fucini / Shigeyuki Yokoyama / Rajendra K Agrawal /
Abstract: Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ...Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.
History
DepositionSep 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Ribosome-binding factor A
B: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)21,7512
Polymers21,7512
Non-polymers00
Water1,892105
1
A: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)10,8761
Polymers10,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)10,8761
Polymers10,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.426, 65.838, 43.173
Angle α, β, γ (deg.)90.00, 96.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosome-binding factor A


Mass: 10875.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0907 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJV1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2M Ammonium dihydrogen phosphate, 0.08M Tris-HCl pH8.5, 9.6% v/v Glycerol anhydrous, 0.02M Bis-Tris propane pH 7.0, 0.08M Magnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→43 Å / Num. obs: 13813 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 24.4
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.22 / Num. unique all: 1383 / Rsym value: 0.312 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JOS

1jos


Resolution: 1.84→42.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 591976.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 700 5.1 %RANDOM
Rwork0.199 ---
obs0.199 13793 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0221 Å2 / ksol: 0.373731 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å2-4.31 Å2
2---5.75 Å20 Å2
3---2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.84→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 105 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.051.5
X-RAY DIFFRACTIONc_mcangle_it3.752
X-RAY DIFFRACTIONc_scbond_it4.992
X-RAY DIFFRACTIONc_scangle_it72.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 128 5.6 %
Rwork0.249 2164 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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