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- PDB-5wy4: Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5wy4
TitleCrystal structure of Chaetomium thermophilum Utp10 N-terminal domain
ComponentsPutative uncharacterized protein
KeywordsRIBOSOMAL PROTEIN / NUCLEAR PROTEIN / nucleolar protein / components of 90S preribosome
Function / homology
Function and homology information


t-UTP complex / snoRNA binding / positive regulation of transcription by RNA polymerase I / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome
Similarity search - Function
BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / BP28CT (NUC211) domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 10
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.499 Å
AuthorsChen, R. / Zhu, X. / Ye, K.
CitationJournal: To Be Published
Title: Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain
Authors: Chen, R. / Zhu, X. / Ye, K.
History
DepositionJan 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,2281
Polymers52,2281
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15800 Å2
Unit cell
Length a, b, c (Å)81.888, 70.458, 93.728
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 Putative uncharacterized protein / Utp10


Mass: 52228.414 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0024640 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5L1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.59 Å3/Da / Density % sol: 52.48 % / Mosaicity: 0.49 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, 1.0 M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35781 / % possible obs: 98.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.103 / Χ2: 2.201 / Net I/av σ(I): 25.003 / Net I/σ(I): 15.9 / Num. measured all: 168375
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.543.30.46118311.045100
2.54-2.593.90.43217951.113100
2.59-2.644.70.39618381.133100
2.64-2.695.30.34318071.252100
2.69-2.755.30.29918021.277100
2.75-2.825.30.25618101.425100
2.82-2.895.30.22618061.488100
2.89-2.965.30.19618131.626100
2.96-3.055.30.17118201.803100
3.05-3.155.20.14117962.02199.9
3.15-3.265.20.12518372.172100
3.26-3.395.10.10917952.5499.9
3.39-3.554.90.09918382.88599.9
3.55-3.734.80.09217883.14699.7
3.73-3.974.50.08117783.27799
3.97-4.274.30.07417783.28197.8
4.27-4.74.10.06717713.2896.7
4.7-5.384.10.06817683.51197.8
5.38-6.784.20.06517653.32996.9
6.781-503.60.06215453.89585

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIX(1.11rc1_2513: ???)refinement
RefinementMethod to determine structure: SAD / Resolution: 2.499→19.908 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 3570 9.99 %
Rwork0.2221 32165 -
obs0.2263 35735 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.53 Å2 / Biso mean: 51.5149 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: final / Resolution: 2.499→19.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 0 54 2661
Biso mean---53.43 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092659
X-RAY DIFFRACTIONf_angle_d0.9793607
X-RAY DIFFRACTIONf_chiral_restr0.056422
X-RAY DIFFRACTIONf_plane_restr0.006458
X-RAY DIFFRACTIONf_dihedral_angle_d3.3721619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4986-2.53140.30061310.25171190132194
2.5314-2.5660.26431360.248912311367100
2.566-2.60260.31621450.245212811426100
2.6026-2.64130.33771380.253812671405100
2.6413-2.68250.33731330.228112211354100
2.6825-2.72640.28521410.240112751416100
2.7264-2.77330.33231420.236212531395100
2.7733-2.82360.24931410.231612571398100
2.8236-2.87770.30891400.23512301370100
2.8777-2.93630.29591410.239212791420100
2.9363-2.99990.27271360.225412441380100
2.9999-3.06950.31351420.233812501392100
3.0695-3.14590.28051380.231612591397100
3.1459-3.23060.31141360.224112551391100
3.2306-3.32530.23771400.236612541394100
3.3253-3.43210.30161310.201412491380100
3.4321-3.55410.22031460.218612741420100
3.5541-3.69550.27191360.199512411377100
3.6955-3.86260.19881420.196212561398100
3.8626-4.06460.27141330.1951229136298
4.0646-4.31680.22841360.18491225136198
4.3168-4.64620.25311310.1841207133896
4.6462-5.10660.24621370.20181234137198
5.1066-5.82920.23691370.22871230136798
5.8292-7.28390.26181430.2551191133497
7.2839-19.90820.26691180.27661083120186

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