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- PDB-5nnz: Crystal structure of human ODA16 -

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Basic information

Entry
Database: PDB / ID: 5nnz
TitleCrystal structure of human ODA16
ComponentsDynein assembly factor with WDR repeat domains 1
KeywordsTRANSPORT PROTEIN / Cilium / sperm / intraflagellar transport / IFT / ODA16 / outer dynein arms / ODA / primary cilia dyskenisia
Function / homology
Function and homology information


cerebrospinal fluid circulation / outer dynein arm assembly / intraciliary transport / motile cilium / determination of left/right symmetry / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ciliary basal body / cilium / protein polyubiquitination ...cerebrospinal fluid circulation / outer dynein arm assembly / intraciliary transport / motile cilium / determination of left/right symmetry / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ciliary basal body / cilium / protein polyubiquitination / heart development / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsLorentzen, E. / Taschner, T. / Basquin, J.
CitationJournal: Protein Sci. / Year: 2020
Title: Purification and crystal structure of human ODA16: Implications for ciliary import of outer dynein arms by the intraflagellar transport machinery.
Authors: Wang, J. / Taschner, M. / Petriman, N.A. / Andersen, M.B. / Basquin, J. / Bhogaraju, S. / Vetter, M. / Wachter, S. / Lorentzen, A. / Lorentzen, E.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,6642
Polymers91,6642
Non-polymers00
Water2,378132
1
A: Dynein assembly factor with WDR repeat domains 1


Theoretical massNumber of molelcules
Total (without water)45,8321
Polymers45,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynein assembly factor with WDR repeat domains 1


Theoretical massNumber of molelcules
Total (without water)45,8321
Polymers45,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.150, 69.500, 102.150
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dynein assembly factor with WDR repeat domains 1 / Outer row dynein assembly protein 16 homolog / WD repeat-containing protein 69


Mass: 45831.777 Da / Num. of mol.: 2 / Fragment: UNP residues 1-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAW1, WDR69 / Production host: unidentified baculovirus / References: UniProt: Q8N136
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 285 K / Method: evaporation / pH: 8 / Details: 50mM Tris pH 8 and 50mM NaOxalate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18102 / % possible obs: 98 % / Redundancy: 6 % / CC1/2: 0.98 / Rrim(I) all: 0.19 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2798 / CC1/2: 0.4 / Rpim(I) all: 1.35 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIXdev_1647refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZH

5mzh


Resolution: 2.651→57.461 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2836 904 5.45 %
Rwork0.2264 --
obs0.2304 16593 77.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.651→57.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 0 132 5216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055230
X-RAY DIFFRACTIONf_angle_d1.0757114
X-RAY DIFFRACTIONf_dihedral_angle_d15.1321800
X-RAY DIFFRACTIONf_chiral_restr0.048823
X-RAY DIFFRACTIONf_plane_restr0.004905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6837-2.85180.3674320.3165595X-RAY DIFFRACTION17
2.8518-3.07190.30881070.24162055X-RAY DIFFRACTION60
3.0719-3.3810.26971860.21493226X-RAY DIFFRACTION94
3.381-3.87010.29671720.21223234X-RAY DIFFRACTION95
3.8701-4.87540.25341800.21123275X-RAY DIFFRACTION94
4.8754-52.15980.30052040.25833305X-RAY DIFFRACTION94

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