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- PDB-6yrn: Structure of the Chlamydomonas reinhardtii SAS-6 coiled-coil doma... -

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Basic information

Entry
Database: PDB / ID: 6yrn
TitleStructure of the Chlamydomonas reinhardtii SAS-6 coiled-coil domain, P2 crystal form
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centriole / centrosome / cartwheel / coiled coil / complex / alpha helical
Function / homology: / Sas-6-like, oligomerization domain / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / cytoskeleton / identical protein binding / cytoplasm / Centriole protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKantsadi, A.L. / Vakonakis, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European CommissionMSCA 752069 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Structures of SAS-6 coiled coil hold implications for the polarity of the centriolar cartwheel.
Authors: Kantsadi, A.L. / Hatzopoulos, G.N. / Gonczy, P. / Vakonakis, I.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Centriole protein
B: Centriole protein
C: Centriole protein
D: Centriole protein
E: Centriole protein
F: Centriole protein
G: Centriole protein
H: Centriole protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2789
Polymers104,0848
Non-polymers1941
Water1,24369
1
A: Centriole protein
D: Centriole protein
E: Centriole protein
F: Centriole protein


Theoretical massNumber of molelcules
Total (without water)52,0424
Polymers52,0424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centriole protein
C: Centriole protein
G: Centriole protein
H: Centriole protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2365
Polymers52,0424
Non-polymers1941
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.510, 39.532, 158.871
Angle α, β, γ (deg.)90.00, 101.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Centriole protein


Mass: 13010.449 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6, CHLRE_12g516950v5 / Plasmid: pFLOAT
Details (production host): pET-30a derivative, N-terminal His6-tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CQL4
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M carboxylic acid mixture, 0.1 M imidazole / MES buffer 20% v/v ethylene glycol 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.43→84.82 Å / Num. obs: 40623 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.41 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.101 / Rrim(I) all: 0.185 / Net I/σ(I): 3.7
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2015 / CC1/2: 0.492 / Rpim(I) all: 0.601 / Rrim(I) all: 1.065 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRL

6yrl


Resolution: 2.43→81.53 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.474 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.462 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1973 4.9 %RANDOM
Rwork0.282 ---
obs0.283 40269 98.9 %-
Displacement parametersBiso mean: 49.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.6141 Å20 Å23.7817 Å2
2---1.2725 Å20 Å2
3----0.3417 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: 1 / Resolution: 2.43→81.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 7 69 6603
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016546HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128732HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2632SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1180HARMONIC5
X-RAY DIFFRACTIONt_it6546HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion18.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion842SEMIHARMONIC5
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_contact7239SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.45 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3304 -5.46 %
Rwork0.3093 762 -
all0.3104 806 -
obs--93.34 %
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)
15.0193-0.76225.47280.128-0.7196.4863-0.0786-0.06560.1449-0.07950.00580.0196-0.01280.14030.07280.0502-0.0206-0.0198-0.0541-0.0058-0.014-26.79510.624172.9007
23.00580.565.18090.13960.44378.4029-0.01030.2288-0.02150.084-0.02850.0291-0.0160.0520.03880.02320.0283-0.0115-0.0457-0.0472-0.0691-13.01880.9049210.8555
33.7094-0.0594.70230.2203-0.09967.09680.17490.0168-0.3940.05350.1177-0.12360.0703-0.1662-0.29260.00360.02310.0243-0.1654-0.0178-0.0795-13.49471.4916210.3184
43.48380.03843.150.08690.09293.81280.1685-0.1229-0.1554-0.0330.03180.04190.17910.2358-0.20030.1275-0.0144-0.0348-0.1396-0.0155-0.0402-26.78241.073173.3173
57.4788-0.7636.48110.0492-0.6746.50150.13390.4211-0.0005-0.0468-0.05490.02930.05620.6281-0.07890.1649-0.0182-0.09-0.32790.02780.0162-16.55531.8103159.2548
63.768-0.40754.19530.0493-0.27425.6431-0.0292-0.1955-0.0705-0.09590.0572-0.0526-0.1397-0.0334-0.0280.0831-0.0135-0.0226-0.21510.06260.0226-16.28351.23159.1542
76.72760.65855.71090.09160.62516.6773-0.07140.3350.09070.06090.0040.0842-0.0447-0.07650.06740.05240.02420.0188-0.2379-0.0573-0.1043-20.42662.4995224.6471
87.2640.18736.35540.18950.1777.04030.0223-0.1635-0.11350.05630.0528-0.0099-0.0527-0.4715-0.07510.09180.057-0.0052-0.2272-0.0102-0.0844-21.68733.1201224.4259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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