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- PDB-9k9m: X-ray structure of FBB18 from Chlamydomonas reinhardtii. -

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Basic information

Entry
Database: PDB / ID: 9k9m
TitleX-ray structure of FBB18 from Chlamydomonas reinhardtii.
ComponentsFlagellar associated protein
KeywordsMOTOR PROTEIN / dynein
Function / homologyCilia- and flagella-associated protein 298 / Cilia- and flagella-associated protein 298 / regulation of cilium movement / Flagellar associated protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSahashi, Y. / Tanaka, H. / Shimo-Kon, R. / Yamamoto, R. / Kurisu, G. / Kon, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H03665 Japan
Japan Society for the Promotion of Science (JSPS)JP17K15117 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Chlamydomonas FBB18 is a ubiquitin-like protein essential for the cytoplasmic preassembly of various ciliary dyneins.
Authors: Yamamoto, R. / Sahashi, Y. / Shimo-Kon, R. / Sakato-Antoku, M. / Suzuki, M. / Luo, L. / Tanaka, H. / Ishikawa, T. / Yagi, T. / King, S.M. / Kurisu, G. / Kon, T.
History
DepositionOct 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: 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
C: Flagellar associated protein
B: Flagellar associated protein
D: Flagellar associated protein


Theoretical massNumber of molelcules
Total (without water)106,2334
Polymers106,2334
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.954, 152.093, 116.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Flagellar associated protein


Mass: 26558.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_16g688450v5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K3CU42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG8000, 100 mM HEPES (pH7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 91792 / % possible obs: 98 % / Redundancy: 2.8 % / Biso Wilson estimate: 52.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14545 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→34.61 Å / SU ML: 0.3724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5764 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 3752 4.09 %
Rwork0.1982 87992 -
obs0.2003 91744 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 0 118 6587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796581
X-RAY DIFFRACTIONf_angle_d0.95448896
X-RAY DIFFRACTIONf_chiral_restr0.05391004
X-RAY DIFFRACTIONf_plane_restr0.00731163
X-RAY DIFFRACTIONf_dihedral_angle_d4.18164072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.43631270.35753048X-RAY DIFFRACTION91
2.33-2.360.3941370.3473201X-RAY DIFFRACTION97.12
2.36-2.390.35541390.32923272X-RAY DIFFRACTION97.18
2.39-2.430.33711350.31873260X-RAY DIFFRACTION97.75
2.43-2.460.35291360.31363188X-RAY DIFFRACTION97.36
2.46-2.50.40371360.30443257X-RAY DIFFRACTION96.75
2.5-2.540.38411380.28463182X-RAY DIFFRACTION96.99
2.54-2.590.30761400.2663227X-RAY DIFFRACTION95.87
2.59-2.640.31541330.26183193X-RAY DIFFRACTION96.27
2.64-2.690.30471390.263214X-RAY DIFFRACTION97.22
2.69-2.740.33931390.25443279X-RAY DIFFRACTION98.19
2.74-2.80.26271390.24873265X-RAY DIFFRACTION98.87
2.8-2.870.40011460.23893321X-RAY DIFFRACTION99.34
2.87-2.940.2771420.23823294X-RAY DIFFRACTION99.48
2.94-3.020.26971400.23423280X-RAY DIFFRACTION99.45
3.02-3.10.28251460.23623321X-RAY DIFFRACTION99.4
3.1-3.210.31391390.21843299X-RAY DIFFRACTION99.57
3.21-3.320.2731440.22393337X-RAY DIFFRACTION99.6
3.32-3.450.30271410.21473299X-RAY DIFFRACTION99.42
3.45-3.610.23371400.1963345X-RAY DIFFRACTION99.01
3.61-3.80.25391420.19323219X-RAY DIFFRACTION98.74
3.8-4.040.21241400.16713271X-RAY DIFFRACTION98.67
4.04-4.350.21051400.16193299X-RAY DIFFRACTION98.65
4.35-4.790.15731420.14163210X-RAY DIFFRACTION97.24
4.79-5.470.20671380.16233274X-RAY DIFFRACTION97.91
5.47-6.890.2421350.17583316X-RAY DIFFRACTION99.68
6.89-34.610.19341390.14453321X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 61.5561228032 Å / Origin y: 37.6811072045 Å / Origin z: -0.170861886489 Å
111213212223313233
T0.388585635386 Å2-0.00328676390672 Å2-0.0292355800824 Å2-0.426504455815 Å20.00236205354188 Å2--0.486949611701 Å2
L0.103907970327 °20.0765370772948 °2-0.0473914330421 °2-0.738228214812 °2-0.053092944305 °2--0.0218977275959 °2
S-0.073568336246 Å °0.0290831243898 Å °0.0309861645067 Å °0.0388462935351 Å °0.00735174475875 Å °-0.0301630071865 Å °-0.0671646147582 Å °0.0288639771435 Å °0.0737346147695 Å °
Refinement TLS groupSelection details: all

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