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- PDB-5m3q: Crystal structure of Tif6 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 5m3q
TitleCrystal structure of Tif6 from Chaetomium thermophilum
ComponentsEukaryotic translation initiation factor 6
KeywordsRIBOSOME / Ribosome biogenesis / anti-association factor
Function / homology
Function and homology information


ribosomal large subunit binding / ribosomal subunit export from nucleus / translation initiation factor activity / ribosomal large subunit biogenesis / cytosolic ribosome assembly / nucleolus / cytoplasm
Similarity search - Function
L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 6
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsAhmed, Y.L. / Calvino, F.R. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Protein Sci. / Year: 2017
Title: Interaction network of the ribosome assembly machinery from a eukaryotic thermophile.
Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. ...Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. / Thomson, E. / Flemming, D. / Sinning, I. / Hurt, E.
History
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9146
Polymers27,4421
Non-polymers4725
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-23 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.350, 63.372, 78.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 27441.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: TIF6, CTHT_0025830 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S683
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Na-citrate pH 5.6 0.5 M Ammonium sulfate 1 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→44.72 Å / Num. obs: 43931 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.031 / Rrim(I) all: 0.07 / Net I/σ(I): 16.8 / Num. measured all: 212576 / Scaling rejects: 49
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.533.10.61630520270.6450.3840.7252.494.2
8.22-44.723.90.02712503230.9980.0150.03138.198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.531
Highest resolutionLowest resolution
Rotation44.72 Å1.68 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.17data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G62

1g62


Resolution: 1.5→41.256 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 2194 5 %
Rwork0.1501 41676 -
obs0.1514 43870 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 19.6297 Å2 / Biso min: 6.08 Å2
Refinement stepCycle: final / Resolution: 1.5→41.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 27 248 1971
Biso mean--41.61 34.81 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171870
X-RAY DIFFRACTIONf_angle_d1.5692566
X-RAY DIFFRACTIONf_chiral_restr0.103307
X-RAY DIFFRACTIONf_plane_restr0.009342
X-RAY DIFFRACTIONf_dihedral_angle_d14.4131126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.53270.27231280.23392420254894
1.5327-1.56830.21011280.1992499262796
1.5683-1.60760.21061320.17242572270499
1.6076-1.6510.18911340.163126022736100
1.651-1.69960.17031390.157525892728100
1.6996-1.75450.20721500.153225622712100
1.7545-1.81720.19681450.153226162761100
1.8172-1.88990.17541260.149225912717100
1.8899-1.97590.16231480.138526022750100
1.9759-2.08010.15621360.137326132749100
2.0801-2.21040.16511370.138626032740100
2.2104-2.38110.17231360.145626402776100
2.3811-2.62070.1781360.153226302766100
2.6207-2.99980.18141470.154226482795100
2.9998-3.7790.16121340.137426812815100
3.779-41.27120.17381380.14752808294699
Refinement TLS params.Method: refined / Origin x: -7.0998 Å / Origin y: 14.1623 Å / Origin z: 7.4883 Å
111213212223313233
T0.0415 Å2-0.0053 Å2-0.0018 Å2-0.047 Å20.0004 Å2--0.0451 Å2
L0.484 °2-0.0826 °20.1886 °2-0.5373 °2-0.2114 °2--0.5223 °2
S-0.013 Å °-0.0085 Å °0.0109 Å °-0.0162 Å °0.0167 Å °0.0462 Å °0.0286 Å °-0.0071 Å °-0.0132 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 225
2X-RAY DIFFRACTION1allB1 - 3
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 248

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