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- PDB-6qt8: Crystal structure of Rea1-MIDAS domain from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 6qt8
TitleCrystal structure of Rea1-MIDAS domain from Chaetomium thermophilum
ComponentsMidasinMDN1
KeywordsRIBOSOME / ribosome biogenesis / integrin / midas
Function / homology
Function and homology information


nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding
Similarity search - Function
Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor (vWF) type A domain ...Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / Midasin
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsAhmed, Y.L. / Thoms, M. / Hurt, E. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin-ligand-type complexes.
Authors: Ahmed, Y.L. / Thoms, M. / Mitterer, V. / Sinning, I. / Hurt, E.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Midasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,20712
Polymers38,0691
Non-polymers1,13711
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-55 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.853, 85.853, 156.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Midasin / MDN1


Mass: 38069.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0069750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SHE6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.48 M (NH4)2SO4, 5 mM MgCl2 and 10 mM NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97264 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 2.33→44.54 Å / Num. obs: 47603 / % possible obs: 99.79 % / Redundancy: 4.2 % / Biso Wilson estimate: 57.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.09
Reflection shellResolution: 2.33→2.41 Å / CC1/2: 0.414

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
REFMACrefinement
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.33→44.54 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2121 2406 5.05 %
Rwork0.1815 --
obs0.1831 47598 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 227.15 Å2 / Biso mean: 82.4017 Å2 / Biso min: 35.81 Å2
Refinement stepCycle: final / Resolution: 2.33→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 46 23 2360
Biso mean--121.81 87.54 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082368
X-RAY DIFFRACTIONf_angle_d0.9953201
X-RAY DIFFRACTIONf_chiral_restr0.054363
X-RAY DIFFRACTIONf_plane_restr0.006403
X-RAY DIFFRACTIONf_dihedral_angle_d14.7641426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.37760.35431350.29626802815100
2.3776-2.42930.30961280.28132644277299
2.4293-2.48580.31551210.258626742795100
2.4858-2.54790.27081530.241526532806100
2.5479-2.61680.30951300.239726662796100
2.6168-2.69380.26861290.217226982827100
2.6938-2.78070.26671400.218426582798100
2.7807-2.88010.22891140.217626752789100
2.8801-2.99540.28221740.209726172791100
2.9954-3.13170.25511150.20226972812100
3.1317-3.29680.20131360.189626792815100
3.2968-3.50330.2181590.167626152774100
3.5033-3.77370.21031470.156826682815100
3.7737-4.15320.18411300.157426572787100
4.1532-4.75380.16791680.137626472815100
4.7538-5.98740.18841610.175926282789100
5.9874-47.95240.20261660.183526362802100
Refinement TLS params.Method: refined / Origin x: 65.0996 Å / Origin y: 28.8315 Å / Origin z: 23.5683 Å
111213212223313233
T0.4272 Å2-0.0692 Å20.0441 Å2-0.2319 Å2-0.01 Å2--0.34 Å2
L1.4542 °2-0.0663 °2-0.0975 °2-1.8281 °2-1.0045 °2--2.8865 °2
S0.0529 Å °0.0441 Å °0.0639 Å °-0.4808 Å °0.0073 Å °-0.0389 Å °-0.029 Å °-0.0472 Å °0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4693 - 5000
2X-RAY DIFFRACTION1allA5101
3X-RAY DIFFRACTION1allA5102
4X-RAY DIFFRACTION1allA5103
5X-RAY DIFFRACTION1allA5109 - 5111

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