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- PDB-4tty: N-terminal domain of C. Reinhardtii SAS-6 homolog bld12p G94D F14... -

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Basic information

Entry
Database: PDB / ID: 4tty
TitleN-terminal domain of C. Reinhardtii SAS-6 homolog bld12p G94D F145W Q147R (NN25)
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centriole SAS-6 / cartwheel / beta-sandwich / alpha-beta protein
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: 1.9 Å
AuthorsHilbert, M. / Kraatz, S.H.W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
CitationJournal: 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.
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

Downloads & links

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Assembly

Deposited unit
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,4602
Polymers36,4602
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.200, 44.220, 70.330
Angle α, β, γ (deg.)90.00, 117.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

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Components

#1: Protein Centriole protein / SAS-6 homolog Bld12p


Mass: 18229.754 Da / Num. of mol.: 2 / Fragment: Residues 1-159 / Mutation: G94D F145W Q147R
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.: 333 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
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: 1.9→40.696 Å / Num. obs: 25239 / % possible obs: 98.4 % / Redundancy: 7.5 % / Net I/σ(I): 14.83
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.66 / % possible all: 93.8

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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
Starting model: 3q0y

3q0y


Resolution: 1.9→40.697 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1262 5 %
Rwork0.2097 --
obs0.2115 25222 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→40.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 0 333 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032349
X-RAY DIFFRACTIONf_angle_d0.7743186
X-RAY DIFFRACTIONf_dihedral_angle_d12.084873
X-RAY DIFFRACTIONf_chiral_restr0.03368
X-RAY DIFFRACTIONf_plane_restr0.003411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8975-1.97340.40181330.35242532X-RAY DIFFRACTION95
1.9734-2.06330.29891390.27942613X-RAY DIFFRACTION98
2.0633-2.1720.29191390.25912649X-RAY DIFFRACTION98
2.172-2.30810.2751410.2382670X-RAY DIFFRACTION99
2.3081-2.48630.31221380.22722635X-RAY DIFFRACTION99
2.4863-2.73650.28461410.22452681X-RAY DIFFRACTION99
2.7365-3.13230.22191420.19862692X-RAY DIFFRACTION99
3.1323-3.94580.20871420.17712713X-RAY DIFFRACTION99
3.9458-40.70670.21141470.18332775X-RAY DIFFRACTION100

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