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- PDB-4ttz: N-terminal domain of C. Reinhardtii SAS-6 homolog bld12p variant ... -

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Basic information

Entry
Database: PDB / ID: 4ttz
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p variant G94E F145W Q147K (NN26)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / stabilization / 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: 2.5 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 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 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
D: Centriole protein
A: Centriole protein
B: Centriole protein
C: Centriole protein


Theoretical massNumber of molelcules
Total (without water)72,8634
Polymers72,8634
Non-polymers00
Water2,360131
1
D: Centriole protein
C: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,4322
Polymers36,4322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area14980 Å2
MethodPISA
2
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,4322
Polymers36,4322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.510, 40.110, 142.490
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: 18215.768 Da / Num. of mol.: 4 / Fragment: N-terminal domain, residues 1-159 / Mutation: G94E F145W Q147K
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.: 131 / 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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→71.25 Å / Num. obs: 19737 / % possible obs: 99.1 % / Redundancy: 14.1 % / Net I/σ(I): 23.94
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 2.66 / % possible all: 87.9

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Processing

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

3q0y


Resolution: 2.5→71.245 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 987 5 %
Rwork0.2071 --
obs0.2094 19736 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→71.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 0 131 4629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024594
X-RAY DIFFRACTIONf_angle_d0.5166222
X-RAY DIFFRACTIONf_dihedral_angle_d8.9521708
X-RAY DIFFRACTIONf_chiral_restr0.019723
X-RAY DIFFRACTIONf_plane_restr0.003793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4996-2.63140.31331290.26362453X-RAY DIFFRACTION94
2.6314-2.79630.34591390.25182653X-RAY DIFFRACTION100
2.7963-3.01220.29111410.25112670X-RAY DIFFRACTION100
3.0122-3.31530.29851410.2292675X-RAY DIFFRACTION100
3.3153-3.7950.26381410.20242690X-RAY DIFFRACTION100
3.795-4.78120.21321440.17052732X-RAY DIFFRACTION100
4.7812-71.27390.20981520.1982876X-RAY DIFFRACTION100

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