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- PDB-5mzh: Crystal structure of ODA16 from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 5mzh
TitleCrystal structure of ODA16 from Chlamydomonas reinhardtii
ComponentsDynein assembly factor with WDR repeat domains 1
KeywordsMOTOR PROTEIN / Intraflagellar transport / cilium / beta propeller / cargo adaptor
Function / homology
Function and homology information


outer dynein arm assembly / intraciliary transport / motile cilium / ciliary basal body / cilium / cytoplasm
Similarity search - Function
G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Dynein assembly factor with WD repeat domains 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsLorentzen, E. / Taschner, M. / Basquin, J. / Mourao, A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis of outer dynein arm intraflagellar transport by the transport adaptor protein ODA16 and the intraflagellar transport protein IFT46.
Authors: Taschner, M. / Mourao, A. / Awasthi, M. / Basquin, J. / Lorentzen, E.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein assembly factor with WDR repeat domains 1
B: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5635
Polymers100,2752
Non-polymers2883
Water5,134285
1
A: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3303
Polymers50,1371
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2332
Polymers50,1371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.767, 62.767, 460.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Dynein assembly factor with WDR repeat domains 1 / Outer row dynein assembly protein 16


Mass: 50137.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: DAW1, ODA16 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3Y8L7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 300 mM ammonium sulfate and 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49 Å / Num. obs: 39781 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rpim(I) all: 0.125 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.8 / Num. unique all: 3718 / Rpim(I) all: 0.884 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wjs

4wjs


Resolution: 2.398→49.154 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2199 2011 5.06 %
Rwork0.1577 --
obs0.1609 39774 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→49.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 15 285 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086635
X-RAY DIFFRACTIONf_angle_d1.1089014
X-RAY DIFFRACTIONf_dihedral_angle_d14.2233898
X-RAY DIFFRACTIONf_chiral_restr0.0631031
X-RAY DIFFRACTIONf_plane_restr0.0071152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31011070.24682663X-RAY DIFFRACTION95
2.46-2.52650.32161830.24662713X-RAY DIFFRACTION94
2.5265-2.60080.3381570.23662659X-RAY DIFFRACTION94
2.6008-2.68460.30141440.22232654X-RAY DIFFRACTION95
2.6846-2.78050.28921290.21472721X-RAY DIFFRACTION95
2.7805-2.89170.30571600.19922666X-RAY DIFFRACTION94
2.8917-3.02320.26091370.18612747X-RAY DIFFRACTION95
3.0232-3.18230.25131430.16772694X-RAY DIFFRACTION95
3.1823-3.38140.21261620.15942675X-RAY DIFFRACTION94
3.3814-3.64190.19741300.14472713X-RAY DIFFRACTION95
3.6419-4.00740.20631540.13422677X-RAY DIFFRACTION95
4.0074-4.5850.15021350.11392701X-RAY DIFFRACTION95
4.585-5.76790.17211440.11692721X-RAY DIFFRACTION95
5.7679-27.55570.16061260.14332723X-RAY DIFFRACTION96

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