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- PDB-5yxm: Crystal structure of Chlamydomonas Outer Arm Dynein Light Chain 1 -

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Basic information

Entry
Database: PDB / ID: 5yxm
TitleCrystal structure of Chlamydomonas Outer Arm Dynein Light Chain 1
ComponentsDynein light chain 1, axonemal
KeywordsCONTRACTILE PROTEIN / MOTOR PROTEIN
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / dynein heavy chain binding / motile cilium / alpha-tubulin binding / microtubule
Similarity search - Function
Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Dynein axonemal light chain 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.545 Å
AuthorsToda, A. / Tanaka, H. / Nishikawa, Y. / Yagi, T. / Kurisu, G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grant-in-Aid for JSPS Fellows17J075530 Japan
Grant-in-Aid for Scientific Research(B)26291014 Japan
CitationJournal: Biophys Rev / Year: 2018
Title: Structural atlas of dynein motors at atomic resolution.
Authors: Toda, A. / Tanaka, H. / Kurisu, G.
History
DepositionDec 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, axonemal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8764
Polymers22,5911
Non-polymers2853
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-12 kcal/mol
Surface area9710 Å2
Unit cell
Length a, b, c (Å)53.536, 69.230, 74.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dynein light chain 1, axonemal / DNAL1 / Flagellar outer arm dynein light chain 1 / ODA-LC protein LC1


Mass: 22591.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LC1, CHLREDRAFT_186669 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XHH2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.545→50 Å / Num. obs: 41149 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 36.49
Reflection shellResolution: 1.545→1.58 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 2043 / CC1/2: 0.734 / Rpim(I) all: 0.384 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data scaling
BALBESphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9N, 3OZX

1a9n

3ozx


Resolution: 1.545→36.85 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.48
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2020 4.92 %Random
Rwork0.1693 ---
obs0.1703 41088 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.31 Å2
Refinement stepCycle: LAST / Resolution: 1.545→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 15 204 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081648
X-RAY DIFFRACTIONf_angle_d1.0312245
X-RAY DIFFRACTIONf_dihedral_angle_d8.6211423
X-RAY DIFFRACTIONf_chiral_restr0.067265
X-RAY DIFFRACTIONf_plane_restr0.006287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5445-1.58310.24081270.23542472X-RAY DIFFRACTION89
1.5831-1.6260.24111270.21092814X-RAY DIFFRACTION100
1.626-1.67380.24071420.19962773X-RAY DIFFRACTION100
1.6738-1.72780.19091420.18342796X-RAY DIFFRACTION100
1.7278-1.78960.18851230.18092801X-RAY DIFFRACTION100
1.7896-1.86120.19651290.16792778X-RAY DIFFRACTION100
1.8612-1.94590.18381480.17132785X-RAY DIFFRACTION100
1.9459-2.04850.19951600.16122795X-RAY DIFFRACTION100
2.0485-2.17680.17311690.15982768X-RAY DIFFRACTION100
2.1768-2.34490.19311600.15642812X-RAY DIFFRACTION100
2.3449-2.58080.19191490.16132821X-RAY DIFFRACTION100
2.5808-2.95410.18961470.17372847X-RAY DIFFRACTION100
2.9541-3.72130.19231350.17192878X-RAY DIFFRACTION100
3.7213-36.86090.16881620.15782928X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9881-0.2027-1.04674.5942-0.39970.2612-0.00490.01580.03330.01310.19630.6428-0.0995-0.4494-0.13260.140.04170.00780.1970.05120.22526.079670.434326.3632
25.37311.563-0.85428.383-1.4082.63610.0219-0.33340.1220.68690.07110.1721-0.449-0.4114-0.05480.29190.06650.03770.2021-0.02040.164611.899975.753136.3195
33.15741.01410.97335.02560.87934.50820.039-0.02010.05380.13770.02850.1951-0.124-0.2577-0.04660.08080.0160.02090.09610.00990.120514.685169.496226.5886
43.80062.11650.99965.49650.27773.8080.01460.01850.07080.0174-0.0410-0.1708-0.02870.02380.06070.020.01440.07630.00940.08220.626966.889824.8734
56.44873.68642.13988.62532.95936.8843-0.0980.33850.101-0.33830.0979-0.4114-0.2920.3627-0.00890.09920.03110.01480.12740.05050.129328.140366.905120.1017
64.13031.2367-0.19476.98250.80183.10630.0608-0.0049-0.03010.0499-0.104-0.0807-0.0725-0.05720.05870.04640.01770.00570.06630.02710.067825.553859.849626.7934
72.4659-0.9960.1544.10640.6691.45670.00380.07790.1567-0.106-0.0348-0.2652-0.06040.16050.02190.091-0.0082-0.00490.11010.01910.084633.304657.19424.3677
86.61220.5473-3.25312.08572.89267.40270.0676-0.42730.48830.14960.126-0.4369-0.37330.4966-0.25490.1747-0.0099-0.05590.1655-0.0220.253438.483961.229531.8644
90.9236-0.82730.98165.62311.01663.02010.060.0411-0.11370.0451-0.007-0.02310.1730.1217-0.05180.07040.00410.01010.1025-0.00260.093834.26742.875428.221
102.8840.924-3.91512.2767-0.48856.75170.1002-0.20860.35530.124-0.0496-0.3538-0.6360.7166-0.15760.17-0.0542-0.05790.2226-0.00960.191142.412153.398232.6919
115.858-3.77245.19073.8364-3.72144.6134-0.0732-0.3199-0.14490.19810.11480.0802-0.0944-0.2824-0.06030.12570.0145-0.01610.1484-0.00160.121436.621548.172138.9949
127.328-4.9846-2.19565.35455.08897.54270.34430.41460.4926-0.9815-0.068-0.7733-0.66370.2767-0.21290.2674-0.04420.02910.2214-0.01020.235548.361447.221235.6788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 3:17
2X-RAY DIFFRACTION2chain A and resid 18:26
3X-RAY DIFFRACTION3chain A and resid 27:55
4X-RAY DIFFRACTION4chain A and resid 56:81
5X-RAY DIFFRACTION5chain A and resid 82:93
6X-RAY DIFFRACTION6chain A and resid 94:106
7X-RAY DIFFRACTION7chain A and resid 107:135
8X-RAY DIFFRACTION8chain A and resid 136:144
9X-RAY DIFFRACTION9chain A and resid 145:169
10X-RAY DIFFRACTION10chain A and resid 170:177
11X-RAY DIFFRACTION11chain A and resid 178:188
12X-RAY DIFFRACTION12chain A and resid 189:196

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