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- PDB-7a3z: OSM-3 kinesin motor domain complexed with Mg.ADP -

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Basic information

Entry
Database: PDB / ID: 7a3z
TitleOSM-3 kinesin motor domain complexed with Mg.ADP
ComponentsOsmotic avoidance abnormal protein 3
KeywordsMOTOR PROTEIN / Kinesin-2 / Kif17 / motor domain / ATPase
Function / homology
Function and homology information


dauer entry / positive regulation of dauer larval development / negative regulation of non-motile cilium assembly / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / intraciliary transport / regulation of insulin receptor signaling pathway / anterograde dendritic transport of neurotransmitter receptor complex / cell projection organization ...dauer entry / positive regulation of dauer larval development / negative regulation of non-motile cilium assembly / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / intraciliary transport / regulation of insulin receptor signaling pathway / anterograde dendritic transport of neurotransmitter receptor complex / cell projection organization / non-motile cilium assembly / non-motile cilium / plus-end-directed microtubule motor activity / microtubule organizing center / kinesin complex / microtubule motor activity / cilium assembly / dendrite cytoplasm / ciliary basal body / cilium / microtubule binding / microtubule / neuron projection / dendrite / neuronal cell body / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Osmotic avoidance abnormal protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsVarela, F.P. / Menetrey, J. / Gigant, B.
CitationJournal: Febs Open Bio / Year: 2021
Title: Structural snapshots of the kinesin-2 OSM-3 along its nucleotide cycle: implications for the ATP hydrolysis mechanism.
Authors: Varela, P.F. / Chenon, M. / Velours, C. / Verhey, K.J. / Menetrey, J. / Gigant, B.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5603
Polymers41,1081
Non-polymers4522
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-17 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.890, 62.110, 45.030
Angle α, β, γ (deg.)90.000, 90.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Osmotic avoidance abnormal protein 3 / Kinesin-like protein osm-3


Mass: 41108.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: osm-3, M02B7.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46873
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M KNO3 and 20% (W/V) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.976411 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976411 Å / Relative weight: 1
ReflectionResolution: 2.09→45.03 Å / Num. obs: 22197 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rrim(I) all: 0.188 / Net I/σ(I): 7.5
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3477 / CC1/2: 0.394 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B6U

3b6u


Resolution: 2.095→45.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1110 5 %RANDOM
Rwork0.2109 ---
obs0.2128 22197 99.3 %-
Displacement parametersBiso max: 101.22 Å2 / Biso mean: 52.49 Å2 / Biso min: 31.71 Å2
Baniso -1Baniso -2Baniso -3
1--9.0265 Å20 Å23.2131 Å2
2--2.4803 Å20 Å2
3---6.5462 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.095→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 28 141 2477
Biso mean--41.33 50.56 -
Num. residues----307
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d805SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it2372HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1863SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2372HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3220HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.42
LS refinement shellResolution: 2.1→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2541 22 4.95 %
Rwork0.2808 422 -
all0.2795 444 -
obs--86.93 %
Refinement TLS params.Method: refined / Origin x: 5.1823 Å / Origin y: 1.2757 Å / Origin z: 15.6714 Å
111213212223313233
T-0.4234 Å20.0361 Å20.0277 Å2--0.3068 Å2-0.0454 Å2---0.2532 Å2
L1.18 °20.124 °20.3853 °2-1.4723 °2-0.1254 °2--1.7575 °2
S0.0118 Å °-0.1352 Å °0.0665 Å °0.0474 Å °-0.0252 Å °0.5532 Å °-0.0873 Å °-0.6921 Å °0.0134 Å °
Refinement TLS groupSelection details: { A|* }

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