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- PDB-5n1a: Crystal structure of Utp4 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 5n1a
TitleCrystal structure of Utp4 from Chaetomium thermophilum
Componentsutp4
KeywordsTRANSLATION / Ribosome biogenesis / RIBOSOME
Function / homology
Function and homology information


t-UTP complex / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / RNA binding
Similarity search - Function
Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Trp-Asp (WD) repeats profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsCalvino, F.R. / Ahmed, Y.L. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: PLoS ONE / Year: 2017
Title: Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis.
Authors: Calvino, F.R. / Kornprobst, M. / Schermann, G. / Birkle, F. / Wild, K. / Fischer, T. / Hurt, E. / Ahmed, Y.L. / Sinning, I.
History
DepositionFeb 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: utp4
B: utp4


Theoretical massNumber of molelcules
Total (without water)202,9432
Polymers202,9432
Non-polymers00
Water11,674648
1
A: utp4


Theoretical massNumber of molelcules
Total (without water)101,4721
Polymers101,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: utp4


Theoretical massNumber of molelcules
Total (without water)101,4721
Polymers101,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.027, 81.593, 112.300
Angle α, β, γ (deg.)90.000, 110.550, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -10 through 32 or resid 35...
21(chain B and (resid -10 through 141 or resid 148...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -10 through 32 or resid 35...A-10 - 32
121(chain A and (resid -10 through 32 or resid 35...A35 - 182
131(chain A and (resid -10 through 32 or resid 35...A184 - 323
141(chain A and (resid -10 through 32 or resid 35...A325 - 398
151(chain A and (resid -10 through 32 or resid 35...A416 - 578
161(chain A and (resid -10 through 32 or resid 35...A611 - 615
171(chain A and (resid -10 through 32 or resid 35...A617 - 868
211(chain B and (resid -10 through 141 or resid 148...B-10 - 141
221(chain B and (resid -10 through 141 or resid 148...B148 - 323
231(chain B and (resid -10 through 141 or resid 148...B325 - 615
241(chain B and (resid -10 through 141 or resid 148...B617 - 868

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Components

#1: Protein utp4


Mass: 101471.656 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)
Gene: CTHT_0058380 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SCT7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5% (w/v) 2-methyl-1,5-pentane-diol (MPD) 100 mM Tris-HCl pH 85

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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: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.15→47.53 Å / Num. obs: 93437 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 34.66 Å2 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47.528 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 9150 4.99 %
Rwork0.1834 174066 -
obs0.1852 183216 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.88 Å2 / Biso mean: 42.4917 Å2 / Biso min: 17.93 Å2
Refinement stepCycle: final / Resolution: 2.15→47.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11051 0 0 648 11699
Biso mean---42.87 -
Num. residues----1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411336
X-RAY DIFFRACTIONf_angle_d1.01615371
X-RAY DIFFRACTIONf_chiral_restr0.0561699
X-RAY DIFFRACTIONf_plane_restr0.0051951
X-RAY DIFFRACTIONf_dihedral_angle_d6.5959341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6236X-RAY DIFFRACTION9.458TORSIONAL
12B6236X-RAY DIFFRACTION9.458TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17440.30223140.281156725986100
2.1744-2.20.3383310.279258166147100
2.2-2.22690.31682820.260558046086100
2.2269-2.2550.28453210.254357706091100
2.255-2.28470.30043230.258958016124100
2.2847-2.3160.29083300.241957696099100
2.316-2.34910.29143160.24857976113100
2.3491-2.38420.25523380.242158136151100
2.3842-2.42140.26893150.228157396054100
2.4214-2.46110.27263220.228657696091100
2.4611-2.50350.26183240.222958096133100
2.5035-2.54910.26192900.212359146204100
2.5491-2.59810.24953190.214957096028100
2.5981-2.65110.25243230.206457876110100
2.6511-2.70880.25663050.202158126117100
2.7088-2.77180.23843270.202858156142100
2.7718-2.84110.26313180.192257976115100
2.8411-2.91790.23072700.188858296099100
2.9179-3.00370.23393150.19158426157100
3.0037-3.10070.2342990.18457986097100
3.1007-3.21150.21952840.178458476131100
3.2115-3.340.22492700.17858216091100
3.34-3.4920.19753190.17157966115100
3.492-3.6760.1813010.169458566157100
3.676-3.90620.18722990.164758396138100
3.9062-4.20770.17382880.152758226110100
4.2077-4.63080.18532650.133858046069100
4.6308-5.30010.1753030.142558306133100
5.3001-6.67460.20732810.174358206101100
6.6746-47.53970.18752580.17685769602798
Refinement TLS params.Method: refined / Origin x: 57.5578 Å / Origin y: 44.7699 Å / Origin z: 47.2631 Å
111213212223313233
T0.1524 Å20.0059 Å2-0.0091 Å2-0.1849 Å2-0.0325 Å2--0.2076 Å2
L0.2257 °20.0198 °20.0048 °2-0.303 °20.0048 °2--0.2481 °2
S0.0152 Å °0.0083 Å °-0.0031 Å °-0.0274 Å °-0.0363 Å °0.1028 Å °0.0023 Å °-0.0541 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-10 - 868
2X-RAY DIFFRACTION1allB-11 - 869
3X-RAY DIFFRACTION1allS1 - 648

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