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- PDB-5ams: Crystal structure of Sqt1 -

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Basic information

Entry
Database: PDB / ID: 5ams
TitleCrystal structure of Sqt1
ComponentsRIBOSOME ASSEMBLY PROTEIN SQT1
KeywordsCHAPERONE / SQT1 / RIBOSOME / UL16
Function / homology
Function and homology information


ribosomal large subunit biogenesis / ribosomal large subunit assembly / unfolded protein binding / cytosol / cytoplasm
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ribosome assembly protein SQT1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å
AuthorsFrenois, F. / Legrand, P. / Fribourg, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Sqt1P is an Eight-Bladed Wd40 Protein
Authors: Frenois, F. / Legrand, P. / Fribourg, S.
History
DepositionAug 31, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOME ASSEMBLY PROTEIN SQT1
B: RIBOSOME ASSEMBLY PROTEIN SQT1


Theoretical massNumber of molelcules
Total (without water)94,4032
Polymers94,4032
Non-polymers00
Water181
1
A: RIBOSOME ASSEMBLY PROTEIN SQT1


Theoretical massNumber of molelcules
Total (without water)47,2021
Polymers47,2021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBOSOME ASSEMBLY PROTEIN SQT1


Theoretical massNumber of molelcules
Total (without water)47,2021
Polymers47,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.999, 165.999, 95.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBOSOME ASSEMBLY PROTEIN SQT1 / SQT1


Mass: 47201.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P35184
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4 Å3/Da / Density % sol: 70 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97883
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 3.35→47.9 Å / Num. obs: 22101 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 105.91 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 3.35→3.62 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.35→36.37 Å / Cor.coef. Fo:Fc: 0.9644 / Cor.coef. Fo:Fc free: 0.9422 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1087 4.96 %RANDOM
Rwork0.1713 ---
obs0.1738 21896 99.18 %-
Displacement parametersBiso mean: 157.27 Å2
Baniso -1Baniso -2Baniso -3
1-16.5458 Å20 Å20 Å2
2--16.5458 Å20 Å2
3----33.0916 Å2
Refine analyzeLuzzati coordinate error obs: 0.932 Å
Refinement stepCycle: LAST / Resolution: 3.35→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 0 1 5880
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016001HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.428143HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2034SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes866HARMONIC5
X-RAY DIFFRACTIONt_it6001HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion23.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion793SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7092SEMIHARMONIC4
LS refinement shellResolution: 3.35→3.51 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2788 154 5.31 %
Rwork0.2318 2745 -
all0.2343 2899 -
obs--99.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.716-1.40320.02884.4163-0.55642.9576-0.39340.35620.9499-0.13530.1072-0.61330.18320.21630.2862-0.5907-0.0572-0.186-0.39610.0860.745732.278-63.229913.6231
24.87590.1691.09263.6893-0.17172.145-0.3010.56820.5225-0.30180.1492-0.0868-0.0710.13640.1518-0.4771-0.1064-0.1698-0.34220.28360.7386-7.8551-48.6038-6.1198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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