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- PDB-4to7: N-Terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E F14... -

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Basic information

Entry
Database: PDB / ID: 4to7
TitleN-Terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E F145W K146R (NN24)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / SAS-6 / cartwheel
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: 1.252 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 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 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


Theoretical massNumber of molelcules
Total (without water)18,1721
Polymers18,1721
Non-polymers00
Water2,558142
1
A: Centriole protein

A: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)42.460, 67.360, 104.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

21A-277-

HOH

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Components

#1: Protein Centriole protein


Mass: 18171.654 Da / Num. of mol.: 1 / Mutation: Q93E, K146R, F145W
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.: 142 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
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: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.25→52.1 Å / Num. obs: 41536 / % possible obs: 98.7 % / Redundancy: 12.4 % / Net I/σ(I): 17.42
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 12 % / Rmerge(I) obs: 5.916 / Mean I/σ(I) obs: 0.44 / % possible all: 84

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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: 3qoy

3qoy


Resolution: 1.252→19.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 2057 5 %
Rwork0.1671 --
obs0.1681 41116 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.252→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 142 1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091218
X-RAY DIFFRACTIONf_angle_d1.2461669
X-RAY DIFFRACTIONf_dihedral_angle_d13.778470
X-RAY DIFFRACTIONf_chiral_restr0.071195
X-RAY DIFFRACTIONf_plane_restr0.006216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2516-1.28070.53061240.57572365X-RAY DIFFRACTION92
1.2807-1.31270.45821310.4662542X-RAY DIFFRACTION99
1.3127-1.34820.45081360.42282563X-RAY DIFFRACTION99
1.3482-1.38790.38471360.34842579X-RAY DIFFRACTION99
1.3879-1.43260.31011370.2862599X-RAY DIFFRACTION99
1.4326-1.48380.27881380.26052580X-RAY DIFFRACTION99
1.4838-1.54320.26551370.23232610X-RAY DIFFRACTION100
1.5432-1.61340.21521380.18612605X-RAY DIFFRACTION100
1.6134-1.69840.18881380.18092619X-RAY DIFFRACTION100
1.6984-1.80480.16211380.16082626X-RAY DIFFRACTION100
1.8048-1.9440.17131370.1522604X-RAY DIFFRACTION100
1.944-2.13940.18391400.14672652X-RAY DIFFRACTION100
2.1394-2.44850.16551390.14762649X-RAY DIFFRACTION100
2.4485-3.08290.17661420.16622685X-RAY DIFFRACTION100
3.0829-19.6620.17191460.14992781X-RAY DIFFRACTION100

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