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- PDB-8axo: Crystal structure of the C-terminal domain of Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 8axo
TitleCrystal structure of the C-terminal domain of Trypanosoma brucei CFAP410
ComponentsTbCFAP410-CTD
KeywordsSTRUCTURAL PROTEIN / Cilia / Flagella / Coiled-coil
Function / homology: / CFAP410 C-terminal domain / cell tip / Leucine-rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / cytoplasm / CFAP410 C-terminal domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.29 Å
AuthorsDong, G. / Stadler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI5960-B2 Austria
CitationJournal: Open Biology / Year: 2024
Title: The C-terminus of CFAP410 forms a tetrameric helical bundle that is essential for its localization to the basal body.
Authors: Stadler, A. / De Liz, L.V. / Gabriel, H.B. / Alonso-Gil, S. / Crickley, R. / Korbula, K. / Zagrovic, B. / Vaughan, S. / Sunter, J.D. / Dong, G.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TbCFAP410-CTD
B: TbCFAP410-CTD


Theoretical massNumber of molelcules
Total (without water)7,8272
Polymers7,8272
Non-polymers00
Water59433
1
A: TbCFAP410-CTD
B: TbCFAP410-CTD

A: TbCFAP410-CTD
B: TbCFAP410-CTD


Theoretical massNumber of molelcules
Total (without water)15,6544
Polymers15,6544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6600 Å2
ΔGint-60 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.107, 40.107, 62.684
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 259 and (name N or name...
d_2ens_1(chain "B" and ((resid 259 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROLEULEUAA259 - 2724 - 17
d_12GLUGLUSERSERAA274 - 27619 - 21
d_13GLUGLULEULEUAA282 - 29027 - 35
d_21PROPROLEULEUBB259 - 2724 - 17
d_22GLUGLUSERSERBB274 - 27619 - 21
d_23GLUGLULEULEUBB282 - 29027 - 35

NCS oper: (Code: givenMatrix: (0.414888869432, -0.817997484866, -0.398431099156), (-0.816003137042, -0.528227217356, 0.234765600509), (-0.402499821565, 0.227719392229, -0.886644106755)Vector: -20. ...NCS oper: (Code: given
Matrix: (0.414888869432, -0.817997484866, -0.398431099156), (-0.816003137042, -0.528227217356, 0.234765600509), (-0.402499821565, 0.227719392229, -0.886644106755)
Vector: -20.6582407499, -35.6908118029, -0.0374757063738)

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Components

#1: Protein/peptide TbCFAP410-CTD


Mass: 3913.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38DI2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.86 Å3/Da / Density % sol: 33.85 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 2.0 M ammonium sulfate, 5% (v/v) iso-propanol / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.29→19.1 Å / Num. obs: 15025 / % possible obs: 99.65 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.046 / Rrim(I) all: 0.14 / Net I/σ(I): 8.16
Reflection shellResolution: 1.29→1.34 Å / Num. unique obs: 1430 / CC1/2: 0.43 / CC star: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.29→19.1 Å / SU ML: 0.1764 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.4872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 1516 10.09 %
Rwork0.186 13505 -
obs0.1882 15021 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.33 Å2
Refinement stepCycle: LAST / Resolution: 1.29→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 0 33 531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047509
X-RAY DIFFRACTIONf_angle_d0.6112692
X-RAY DIFFRACTIONf_chiral_restr0.040892
X-RAY DIFFRACTIONf_plane_restr0.002287
X-RAY DIFFRACTIONf_dihedral_angle_d3.101872
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.602751331809 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.340.36981270.3111168X-RAY DIFFRACTION97.08
1.34-1.380.27751350.24011212X-RAY DIFFRACTION99.93
1.38-1.440.24331300.21961213X-RAY DIFFRACTION100
1.44-1.50.27571350.18531182X-RAY DIFFRACTION99.92
1.5-1.580.21991370.16911238X-RAY DIFFRACTION100
1.58-1.680.19981390.16891215X-RAY DIFFRACTION100
1.68-1.810.23491390.15491229X-RAY DIFFRACTION99.93
1.81-1.990.20511390.17881235X-RAY DIFFRACTION100
1.99-2.280.20181400.1841230X-RAY DIFFRACTION100
2.28-2.870.17371430.17221263X-RAY DIFFRACTION100
2.88-19.10.21211520.19351320X-RAY DIFFRACTION100

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