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- PDB-4u2i: N-terminal domain of C. Rheinhardtii SAS-6 homolog bld12p Q93E G9... -

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Basic information

Entry
Database: PDB / ID: 4u2i
TitleN-terminal domain of C. Rheinhardtii SAS-6 homolog bld12p Q93E G94D K146R Q147R (NN23)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centriole SAS-6 / cartwheel / beta-sandwich / alpha-beta protein / cell cycle
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: 2.281 Å
AuthorsHilbert, M. / Kraatz, S.H.W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
CitationJournal: 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.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 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

Downloads & links

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Assembly

Deposited unit
A: Centriole protein
C: Centriole protein
B: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)72,8794
Polymers72,8794
Non-polymers00
Water4,071226
1
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,4392
Polymers36,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,4392
Polymers36,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.170, 96.630, 142.510
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


Mass: 18219.719 Da / Num. of mol.: 4 / Fragment: UNP residues 1-159
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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, MES mononhydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 25555 / % possible obs: 97.8 % / Redundancy: 9.8 % / Net I/σ(I): 21.46
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.47 / % possible all: 73.2

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Processing

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

3q0y


Resolution: 2.281→48.315 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1278 5 %
Rwork0.2058 --
obs0.2079 25554 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.281→48.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 0 226 4725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034615
X-RAY DIFFRACTIONf_angle_d0.6826255
X-RAY DIFFRACTIONf_dihedral_angle_d12.2681724
X-RAY DIFFRACTIONf_chiral_restr0.027721
X-RAY DIFFRACTIONf_plane_restr0.002814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2811-2.37240.26761170.23532217X-RAY DIFFRACTION81
2.3724-2.48040.31871400.2462674X-RAY DIFFRACTION99
2.4804-2.61120.30771410.24082684X-RAY DIFFRACTION100
2.6112-2.77480.28061430.23092709X-RAY DIFFRACTION100
2.7748-2.9890.28931440.22392738X-RAY DIFFRACTION100
2.989-3.28970.26391450.21272752X-RAY DIFFRACTION100
3.2897-3.76560.24281450.19652758X-RAY DIFFRACTION100
3.7656-4.74360.20841470.17092790X-RAY DIFFRACTION100
4.7436-48.32580.22571560.20622954X-RAY DIFFRACTION100

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