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- PDB-4zoz: Crystal structure of the Chaetomium thermophilum Sqt1 bound to th... -

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Basic information

Entry
Database: PDB / ID: 4zoz
TitleCrystal structure of the Chaetomium thermophilum Sqt1 bound to the N-terminus of the ribosomal protein L10
Components
  • 60S ribosomal protein L10-like protein
  • Sqt1
KeywordsCHAPERONE / ribosomal biogenesis / WD40 - repeat
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily ...: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / 60S ribosomal protein L10-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPausch, P. / Altegoer, F. / Bange, G.
CitationJournal: Nat Commun / Year: 2015
Title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
Authors: Pausch, P. / Singh, U. / Ahmed, Y.L. / Pillet, B. / Murat, G. / Altegoer, F. / Stier, G. / Thoms, M. / Hurt, E. / Sinning, I. / Bange, G. / Kressler, D.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Sqt1
Y: 60S ribosomal protein L10-like protein
B: Sqt1
C: 60S ribosomal protein L10-like protein


Theoretical massNumber of molelcules
Total (without water)107,5334
Polymers107,5334
Non-polymers00
Water10,178565
1
A: Sqt1
Y: 60S ribosomal protein L10-like protein


Theoretical massNumber of molelcules
Total (without water)53,7672
Polymers53,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-2 kcal/mol
Surface area15710 Å2
MethodPISA
2
B: Sqt1
C: 60S ribosomal protein L10-like protein


Theoretical massNumber of molelcules
Total (without water)53,7672
Polymers53,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-2 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.497, 67.178, 72.815
Angle α, β, γ (deg.)89.92, 108.92, 92.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sqt1


Mass: 50297.512 Da / Num. of mol.: 2 / Fragment: UNP residues 54-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0010920 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S0R0
#2: Protein/peptide 60S ribosomal protein L10-like protein / rpL10


Mass: 3469.024 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0063830 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SEI1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M Na/K-phosphate pH 6.2, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→48.33 Å / Num. obs: 87711 / % possible obs: 93.7 % / Redundancy: 3.7 % / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZOY

4zoy


Resolution: 1.7→48.33 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 4692 5.35 %
Rwork0.1912 --
obs0.1925 87711 93.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 0 565 6591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076156
X-RAY DIFFRACTIONf_angle_d1.098376
X-RAY DIFFRACTIONf_dihedral_angle_d13.1132150
X-RAY DIFFRACTIONf_chiral_restr0.047942
X-RAY DIFFRACTIONf_plane_restr0.0061108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6996-1.71890.29811310.27252581X-RAY DIFFRACTION87
1.7189-1.73910.31461440.25742784X-RAY DIFFRACTION93
1.7391-1.76030.2981890.26212741X-RAY DIFFRACTION93
1.7603-1.78260.26192000.25782658X-RAY DIFFRACTION93
1.7826-1.80610.27451760.23892710X-RAY DIFFRACTION93
1.8061-1.83080.27661600.23532787X-RAY DIFFRACTION93
1.8308-1.8570.27691480.22382740X-RAY DIFFRACTION93
1.857-1.88470.23381510.21662732X-RAY DIFFRACTION93
1.8847-1.91410.21841540.20782762X-RAY DIFFRACTION92
1.9141-1.94550.23151820.20832692X-RAY DIFFRACTION93
1.9455-1.97910.27251670.20712756X-RAY DIFFRACTION92
1.9791-2.01510.27161910.20282583X-RAY DIFFRACTION91
2.0151-2.05380.22182080.20782520X-RAY DIFFRACTION87
2.0538-2.09570.24821760.212823X-RAY DIFFRACTION95
2.0957-2.14130.22761710.2012825X-RAY DIFFRACTION95
2.1413-2.19110.2571300.19252790X-RAY DIFFRACTION95
2.1911-2.24590.2241220.19152895X-RAY DIFFRACTION95
2.2459-2.30660.20571420.19552798X-RAY DIFFRACTION95
2.3066-2.37450.21371670.19112829X-RAY DIFFRACTION95
2.3745-2.45110.21521400.19042788X-RAY DIFFRACTION95
2.4511-2.53880.22591690.1992811X-RAY DIFFRACTION95
2.5388-2.64040.22261200.2012814X-RAY DIFFRACTION94
2.6404-2.76060.23291460.2042766X-RAY DIFFRACTION93
2.7606-2.90610.18961020.19142656X-RAY DIFFRACTION88
2.9061-3.08810.22671280.19352896X-RAY DIFFRACTION97
3.0881-3.32650.21771780.17712860X-RAY DIFFRACTION97
3.3265-3.66120.20811310.17452920X-RAY DIFFRACTION97
3.6612-4.19070.1791520.16642839X-RAY DIFFRACTION97
4.1907-5.27880.14941750.15462805X-RAY DIFFRACTION95
5.2788-48.35090.21291420.18892858X-RAY DIFFRACTION96

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