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- PDB-8r9t: Crystal structure of the C-terminal domain of Chlamydomonas reinh... -

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Basic information

Entry
Database: PDB / ID: 8r9t
TitleCrystal structure of the C-terminal domain of Chlamydomonas reinhardtii CFAP410
ComponentsFlagellar associated protein
KeywordsPROTEIN BINDING / Cilia / Flagellum / CFAP410 / tetramer
Function / homologyLeucine-rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / cytoskeleton / cytoplasm / Flagellar associated protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStadler, A. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund 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
DepositionNov 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar associated protein
B: Flagellar associated protein
C: Flagellar associated protein
D: Flagellar associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2635
Polymers16,2234
Non-polymers401
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, static light scattering data confirms the tetrameric assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-58 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.435, 48.097, 53.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide
Flagellar associated protein


Mass: 4055.637 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CYA1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.71 Å3/Da / Density % sol: 28.13 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.02 M CaCl2, 0.1 M sodium acetate (pH 5.0), 30% (v/v) 2-Methyl-2,4-pentanediol

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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-F / 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: 1.4→20 Å / Num. obs: 22256 / % possible obs: 98.2 % / Observed criterion σ(I): 1.1 / Redundancy: 12.5 % / Biso Wilson estimate: 21.67 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Net I/σ(I): 9.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 19011 / CC1/2: 0.75 / CC star: 0.925 / Rpim(I) all: 0.331 / Rrim(I) all: 1.074 / % possible all: 87.57

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.79 Å / SU ML: 0.1353 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 1999 8.98 %
Rwork0.1626 20257 -
obs0.1649 22256 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.89 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 1 91 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871088
X-RAY DIFFRACTIONf_angle_d0.92231460
X-RAY DIFFRACTIONf_chiral_restr0.0456173
X-RAY DIFFRACTIONf_plane_restr0.0038187
X-RAY DIFFRACTIONf_dihedral_angle_d3.7987151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.35131140.27551166X-RAY DIFFRACTION80.45
1.43-1.470.27871390.22761393X-RAY DIFFRACTION95.57
1.47-1.510.24641410.18741436X-RAY DIFFRACTION98.32
1.51-1.560.22171420.1631442X-RAY DIFFRACTION98.75
1.56-1.620.18651430.14431446X-RAY DIFFRACTION98.88
1.62-1.680.1841420.13591435X-RAY DIFFRACTION99.24
1.68-1.760.20681440.14111459X-RAY DIFFRACTION99.38
1.76-1.850.18421440.14411468X-RAY DIFFRACTION99.57
1.85-1.970.20051440.13281450X-RAY DIFFRACTION99.69
1.97-2.120.17461460.13771477X-RAY DIFFRACTION99.69
2.12-2.330.16671450.13011479X-RAY DIFFRACTION99.82
2.33-2.670.16241490.14811502X-RAY DIFFRACTION100
2.67-3.360.20121490.17461511X-RAY DIFFRACTION100
3.36-19.790.18611570.18191593X-RAY DIFFRACTION99.66

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