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- PDB-5o9e: Crystal structure of the Imp4-Mpp10 complex from Chaetomium therm... -

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Basic information

Entry
Database: PDB / ID: 5o9e
TitleCrystal structure of the Imp4-Mpp10 complex from Chaetomium thermophilum
Components
  • Putative U3 small nucleolar ribonucleoprotein
  • Putative U3 small nucleolar ribonucleoprotein protein
KeywordsRIBOSOME / Ribosome biogenesis / BRIX
Function / homology
Function and homology information


Mpp10 complex / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / snoRNA binding / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / nucleoplasm
Similarity search - Function
U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / U3 snoRNP protein/Ribosome production factor 1 / Brix domain / Brix domain / Brix domain profile. / Brix
Similarity search - Domain/homology
Putative U3 small nucleolar ribonucleoprotein protein / U3 small nucleolar ribonucleoprotein protein IMP4
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.884 Å
AuthorsKharde, S. / Ahmed, Y.L. / Sinning, I.
CitationJournal: PLoS ONE / Year: 2017
Title: Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome.
Authors: Sa-Moura, B. / Kornprobst, M. / Kharde, S. / Ahmed, Y.L. / Stier, G. / Kunze, R. / Sinning, I. / Hurt, E.
History
DepositionJun 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 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: Putative U3 small nucleolar ribonucleoprotein
B: Putative U3 small nucleolar ribonucleoprotein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6503
Polymers37,5882
Non-polymers621
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.890, 112.890, 44.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Putative U3 small nucleolar ribonucleoprotein


Mass: 22800.330 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0062900 / Plasmid: pET21g / Details (production host): modified pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SE90
#2: Protein Putative U3 small nucleolar ribonucleoprotein protein


Mass: 14787.353 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0046030 / Plasmid: pETZZ1a / Details (production host): modified pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S9I7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20-30 % Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.88→48.883 Å / Num. obs: 26155 / % possible obs: 99.98 % / Redundancy: 7 % / Biso Wilson estimate: 27.64 Å2 / Net I/σ(I): 9.15

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BY8

5by8


Resolution: 1.884→48.883 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2192 1304 5 %
Rwork0.1836 --
obs0.1853 26075 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.75 Å2 / Biso mean: 35.1536 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 1.884→48.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 4 136 2384
Biso mean--47.38 40.36 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092299
X-RAY DIFFRACTIONf_angle_d0.9353109
X-RAY DIFFRACTIONf_chiral_restr0.065356
X-RAY DIFFRACTIONf_plane_restr0.007405
X-RAY DIFFRACTIONf_dihedral_angle_d10.7481825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8843-1.95970.35621390.30732650278997
1.9597-2.04890.24941440.239527382882100
2.0489-2.1570.23411450.20427402885100
2.157-2.29210.25411440.199927412885100
2.2921-2.46910.221450.181727582903100
2.4691-2.71750.2321450.189927482893100
2.7175-3.11070.21351460.186227792925100
3.1107-3.91890.21171460.17427682914100
3.9189-48.89920.18941500.156428492999100
Refinement TLS params.Method: refined / Origin x: 30.5593 Å / Origin y: 23.2614 Å / Origin z: 33.8023 Å
111213212223313233
T0.1559 Å20.0154 Å20.0003 Å2-0.1609 Å2-0.006 Å2--0.1561 Å2
L0.6142 °20.2458 °2-0.105 °2-1.6929 °2-0.6943 °2--1.0108 °2
S-0.0395 Å °0.0323 Å °0.0679 Å °0.0818 Å °-0.0494 Å °-0.1418 Å °0.0146 Å °0.0015 Å °-0.0081 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA74 - 274
2X-RAY DIFFRACTION1allB475 - 562
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 136

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