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- PDB-4tq7: N-terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E (NN10) -

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Basic information

Entry
Database: PDB / ID: 4tq7
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E (NN10)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centriole SAS-6 / cartwheel / beta-sandwich / alpha-beta protein / centriolar
Function / homologySpindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal / centriole / cell cycle / identical protein binding / cytoplasm / Centriole protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.643 Å
AuthorsHilbert, M. / Kraatz, S.H.W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
Citation
Journal: Nat.Cell Biol. / Year: 2016
Title: SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture.
Authors: Hilbert, M. / Noga, A. / Frey, D. / Hamel, V. / Guichard, P. / Kraatz, S.H. / Pfreundschuh, M. / Hosner, S. / Fluckiger, I. / Jaussi, R. / Wieser, M.M. / Thieltges, K.M. / Deupi, X. / ...Authors: Hilbert, M. / Noga, A. / Frey, D. / Hamel, V. / Guichard, P. / Kraatz, S.H. / Pfreundschuh, M. / Hosner, S. / Fluckiger, I. / Jaussi, R. / Wieser, M.M. / Thieltges, K.M. / Deupi, X. / Muller, D.J. / Kammerer, R.A. / Gonczy, P. / Hirono, M. / Steinmetz, M.O.
#1: Journal: Cell / Year: 2011
Title: Structural basis of the 9-fold symmetry of centrioles.
Authors: Kitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Flueckiger, I. / Goenczy, P. / Steinmetz, M.O.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Dec 20, 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

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Assembly

Deposited unit
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2092
Polymers36,2092
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-5 kcal/mol
Surface area15470 Å2
Unit cell
Length a, b, c (Å)46.050, 73.640, 94.960
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 Centriole protein / / N-terminal domain of C. reinhardtii SAS-6 homolog Bld12p Q93E (NN10)


Mass: 18104.605 Da / Num. of mol.: 2 / Mutation: Q93E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CQL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: PEG3350, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.643→41.435 Å / Num. obs: 9912 / % possible obs: 99.7 % / Redundancy: 12.5 % / Net I/σ(I): 25.06
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 6.26 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q0y

3q0y


Resolution: 2.643→41.435 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 496 5.01 %
Rwork0.2076 --
obs0.2102 9910 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.643→41.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 0 84 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022336
X-RAY DIFFRACTIONf_angle_d0.5913166
X-RAY DIFFRACTIONf_dihedral_angle_d9.636867
X-RAY DIFFRACTIONf_chiral_restr0.022365
X-RAY DIFFRACTIONf_plane_restr0.003412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6431-2.9090.32481200.24872277X-RAY DIFFRACTION99
2.909-3.32980.31521220.23812326X-RAY DIFFRACTION100
3.3298-4.19460.2681240.20542347X-RAY DIFFRACTION100
4.1946-41.440.21211300.18432464X-RAY DIFFRACTION100

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