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- PDB-4u2j: N-terminal domain of C. Reinhardtii SAS-6 homolog bld12p variant ... -

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Basic information

Entry
Database: PDB / ID: 4u2j
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p variant Q93E F145W (NN27)
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 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
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 1.2May 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
C: Centriole protein
D: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)72,5754
Polymers72,5754
Non-polymers00
Water7,332407
1
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2872
Polymers36,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area15540 Å2
MethodPISA
2
C: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2872
Polymers36,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.150, 97.000, 142.810
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: 18143.641 Da / Num. of mol.: 4 / Fragment: UNP residues 1-159 / Mutation: Q93E 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.: 407 / 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: 1.92 Å3/Da / Density % sol: 35.8 %
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: 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→80.241 Å / Num. obs: 38651 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 15.66
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 2.14 / % possible all: 100

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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 / Resolution: 2→80.241 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1933 5 %
Rwork0.1914 --
obs0.1938 38651 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→80.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 0 407 4953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034666
X-RAY DIFFRACTIONf_angle_d0.7696331
X-RAY DIFFRACTIONf_dihedral_angle_d11.611732
X-RAY DIFFRACTIONf_chiral_restr0.029728
X-RAY DIFFRACTIONf_plane_restr0.003819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28621330.25022534X-RAY DIFFRACTION100
2.05-2.10550.29151390.24162637X-RAY DIFFRACTION100
2.1055-2.16740.32431330.24252532X-RAY DIFFRACTION100
2.1674-2.23740.26751380.2252621X-RAY DIFFRACTION100
2.2374-2.31730.23621350.21542559X-RAY DIFFRACTION100
2.3173-2.41010.28191360.21352584X-RAY DIFFRACTION100
2.4101-2.51980.28011380.21692621X-RAY DIFFRACTION100
2.5198-2.65270.2541360.2062592X-RAY DIFFRACTION100
2.6527-2.81890.24431380.19682612X-RAY DIFFRACTION100
2.8189-3.03660.24421380.19562620X-RAY DIFFRACTION100
3.0366-3.34210.24011400.18262660X-RAY DIFFRACTION100
3.3421-3.82580.21251380.1682618X-RAY DIFFRACTION100
3.8258-4.820.17671420.14982703X-RAY DIFFRACTION100
4.82-80.30540.25221490.18882825X-RAY DIFFRACTION100

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