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- PDB-4zn4: Crystal structure of Sqt1 from Chaetomium thermophilum solved by MR -

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Basic information

Entry
Database: PDB / ID: 4zn4
TitleCrystal structure of Sqt1 from Chaetomium thermophilum solved by MR
Componentssqt1
KeywordsCHAPERONE / ribosome biogenesis
Function / homology
Function and homology information


: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsAhmed, Y.L. / Sinning, I.
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 4, 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

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Assembly

Deposited unit
A: sqt1
B: sqt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3475
Polymers114,0672
Non-polymers2803
Water5,495305
1
A: sqt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3144
Polymers57,0341
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: sqt1


Theoretical massNumber of molelcules
Total (without water)57,0341
Polymers57,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.566, 94.823, 94.949
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein sqt1


Mass: 57033.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0010920 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0S0R0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.6M (NH4)2SO4 and 100 mM MES pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.60508 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60508 Å / Relative weight: 1
ReflectionResolution: 1.94→47.41 Å / Num. obs: 67775 / % possible obs: 98.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.027 / Net I/σ(I): 14.6 / Num. measured all: 325940
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.94-1.994.10.7271.91851744780.7130.39796.9
9.1-47.415.20.03536.636416980.9980.01698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation47.41 Å2.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
MOLREP11.0.05phasing
SHELXDEphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ow8

3ow8


Resolution: 1.94→47.411 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 3420 5.05 %
Rwork0.1713 --
obs0.173 67715 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→47.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6019 0 17 305 6341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096188
X-RAY DIFFRACTIONf_angle_d1.2028430
X-RAY DIFFRACTIONf_dihedral_angle_d13.5532144
X-RAY DIFFRACTIONf_chiral_restr0.054956
X-RAY DIFFRACTIONf_plane_restr0.0061114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.96770.28451500.29042575X-RAY DIFFRACTION96
1.9677-1.99710.31631500.27542648X-RAY DIFFRACTION98
1.9971-2.02830.30421490.25522667X-RAY DIFFRACTION98
2.0283-2.06160.27771200.23942691X-RAY DIFFRACTION98
2.0616-2.09710.26451170.23382669X-RAY DIFFRACTION98
2.0971-2.13520.28851350.21782583X-RAY DIFFRACTION96
2.1352-2.17630.25491380.21292641X-RAY DIFFRACTION97
2.1763-2.22070.22061320.19322683X-RAY DIFFRACTION98
2.2207-2.2690.23241420.19212659X-RAY DIFFRACTION99
2.269-2.32180.23551330.19042695X-RAY DIFFRACTION99
2.3218-2.37990.22981330.18532692X-RAY DIFFRACTION99
2.3799-2.44420.23391580.18612689X-RAY DIFFRACTION99
2.4442-2.51610.26561460.19432673X-RAY DIFFRACTION99
2.5161-2.59730.23121280.18092732X-RAY DIFFRACTION99
2.5973-2.69010.21861290.19322691X-RAY DIFFRACTION100
2.6901-2.79780.25411640.2012701X-RAY DIFFRACTION99
2.7978-2.92520.24251390.18432693X-RAY DIFFRACTION99
2.9252-3.07940.20731560.18532668X-RAY DIFFRACTION99
3.0794-3.27220.22441670.17872683X-RAY DIFFRACTION99
3.2722-3.52480.1921670.16092678X-RAY DIFFRACTION99
3.5248-3.87940.17291470.15362673X-RAY DIFFRACTION99
3.8794-4.44040.15491290.13172722X-RAY DIFFRACTION99
4.4404-5.5930.15531380.12752746X-RAY DIFFRACTION99
5.593-47.42560.17291530.15642743X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.4545 Å / Origin y: 71.0445 Å / Origin z: 22.705 Å
111213212223313233
T0.2084 Å20.0644 Å20.0022 Å2-0.233 Å20.0346 Å2--0.1718 Å2
L0.3513 °2-0.2976 °2-0.1047 °2-0.6753 °20.1404 °2--0.0606 °2
S0.1012 Å °0.1521 Å °0.0472 Å °-0.0926 Å °-0.0978 Å °-0.0722 Å °-0.0017 Å °-0.0213 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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