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

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Basic information

Entry
Database: PDB / ID: 4ttx
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p variant G94C K146C (NN19)
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: 2.498 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
A: Centriole protein
B: Centriole protein
C: Centriole protein
D: Centriole protein
E: Centriole protein
F: Centriole protein


Theoretical massNumber of molelcules
Total (without water)108,7426
Polymers108,7426
Non-polymers00
Water13,980776
1
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2472
Polymers36,2472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-13 kcal/mol
Surface area15410 Å2
MethodPISA
2
C: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2472
Polymers36,2472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11 kcal/mol
Surface area15550 Å2
MethodPISA
3
E: Centriole protein
F: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2472
Polymers36,2472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.590, 95.550, 91.430
Angle α, β, γ (deg.)90.00, 112.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Centriole protein


Mass: 18123.674 Da / Num. of mol.: 6 / Fragment: N-terminal domain, Residues 1-159 / Mutation: G94C K146C
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.: 776 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 293 K / Method: evaporation / 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: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→63.26 Å / Num. obs: 48246 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 6.78
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 2.017 / Mean I/σ(I) obs: 0.72 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q0Y

3q0y


Resolution: 2.498→63.257 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 2417 5.01 %
Rwork0.2156 --
obs0.2182 48225 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.498→63.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6934 0 0 776 7710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017083
X-RAY DIFFRACTIONf_angle_d0.489605
X-RAY DIFFRACTIONf_dihedral_angle_d8.2492613
X-RAY DIFFRACTIONf_chiral_restr0.0171111
X-RAY DIFFRACTIONf_plane_restr0.0031250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.498-2.5490.34231310.31632617X-RAY DIFFRACTION97
2.549-2.60440.36111550.31492683X-RAY DIFFRACTION100
2.6044-2.6650.35791330.30122685X-RAY DIFFRACTION100
2.665-2.73160.31911420.28472664X-RAY DIFFRACTION100
2.7316-2.80550.32511410.28132675X-RAY DIFFRACTION100
2.8055-2.8880.35181410.27662694X-RAY DIFFRACTION100
2.888-2.98120.32321450.26562685X-RAY DIFFRACTION100
2.9812-3.08780.32581410.26522700X-RAY DIFFRACTION100
3.0878-3.21140.32131450.24082688X-RAY DIFFRACTION100
3.2114-3.35760.29131400.22782681X-RAY DIFFRACTION100
3.3576-3.53460.28161440.20632720X-RAY DIFFRACTION100
3.5346-3.7560.24711400.20372666X-RAY DIFFRACTION100
3.756-4.0460.23081440.19012733X-RAY DIFFRACTION100
4.046-4.4530.22241420.16722692X-RAY DIFFRACTION100
4.453-5.09710.18311440.15182723X-RAY DIFFRACTION100
5.0971-6.42090.25841430.20632717X-RAY DIFFRACTION100
6.4209-63.27680.22911460.19492785X-RAY DIFFRACTION100

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