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- PDB-4tpz: N-terminal domain of C. Reinhardtii SAS-6 homolog bld12p F145W (NN2) -

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Basic information

Entry
Database: PDB / ID: 4tpz
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p F145W (NN2)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / homodimer / stabilization / mutation / centriole SAS-6 / cartwheel / beta-sandwich / alpha-beta protein / centriolar
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: 1.8 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.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Caenorhabditis elegans centriolar protein SAS-6 forms a spiral that is consistent with imparting a ninefold symmetry.
Authors: Hilbert, M. / Erat, M.C. / Hachet, V. / Guichard, P. / Blank, I.D. / Flueckiger, I. / Slater, L. / Lowe, E.D. / Hatzopoulos, G.N. / Steinmetz, M.O. / Goenczy, P. / Vakonakis, I.
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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)72,5714
Polymers72,5714
Non-polymers00
Water10,719595
1
A: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2852
Polymers36,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area15640 Å2
MethodPISA
2
B: Centriole protein
C: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2852
Polymers36,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.660, 97.630, 143.150
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: 18142.654 Da / Num. of mol.: 4 / Fragment: residues 1-159 / Mutation: 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.: 595 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / Details: PEG6000, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→57.724 Å / Num. obs: 53811 / % possible obs: 99.9 % / Redundancy: 7.37 % / Net I/σ(I): 22.63
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 2.21 / % possible all: 98.9

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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 / Resolution: 1.8→57.724 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2690 5 %
Rwork0.193 --
obs0.1946 53810 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→57.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 0 595 5194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054725
X-RAY DIFFRACTIONf_angle_d1.0926415
X-RAY DIFFRACTIONf_dihedral_angle_d12.3741748
X-RAY DIFFRACTIONf_chiral_restr0.044738
X-RAY DIFFRACTIONf_plane_restr0.006831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83270.29561370.26952605X-RAY DIFFRACTION98
1.8327-1.8680.34761400.26252658X-RAY DIFFRACTION100
1.868-1.90610.32661400.27152652X-RAY DIFFRACTION100
1.9061-1.94760.31991390.25292647X-RAY DIFFRACTION100
1.9476-1.99290.28371400.24492654X-RAY DIFFRACTION100
1.9929-2.04270.25551400.23412675X-RAY DIFFRACTION100
2.0427-2.0980.28351390.22732628X-RAY DIFFRACTION100
2.098-2.15970.25861410.22472686X-RAY DIFFRACTION100
2.1597-2.22940.24641400.20172661X-RAY DIFFRACTION100
2.2294-2.30910.22811410.19832681X-RAY DIFFRACTION100
2.3091-2.40150.21241420.19432690X-RAY DIFFRACTION100
2.4015-2.51080.24791400.19882667X-RAY DIFFRACTION100
2.5108-2.64320.27141410.19552685X-RAY DIFFRACTION100
2.6432-2.80880.2351420.18692685X-RAY DIFFRACTION100
2.8088-3.02570.18831420.18062709X-RAY DIFFRACTION100
3.0257-3.33010.21331430.1772711X-RAY DIFFRACTION100
3.3301-3.81190.20031440.16152739X-RAY DIFFRACTION100
3.8119-4.80230.18821460.14942773X-RAY DIFFRACTION100
4.8023-57.75380.19961530.20812914X-RAY DIFFRACTION100

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