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- PDB-4ynh: Structure of the C. elegans SAS-5 Implico dimerization domain -

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Basic information

Entry
Database: PDB / ID: 4ynh
TitleStructure of the C. elegans SAS-5 Implico dimerization domain
ComponentsSpindle assembly abnormal protein 5
KeywordsSTRUCTURAL PROTEIN / SAS-5 / Centriole / Dimerization domain
Function / homologycentriole assembly / centriole replication / centrosome duplication / centriole / cytoplasm / Spindle assembly abnormal protein 5
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsRogala, K.B. / Vakonakis, I. / Hatzopoulos, G.N.
CitationJournal: Elife / Year: 2015
Title: The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.
Authors: Rogala, K.B. / Dynes, N.J. / Hatzopoulos, G.N. / Yan, J. / Pong, S.K. / Robinson, C.V. / Deane, C.M. / Gonczy, P. / Vakonakis, I.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Spindle assembly abnormal protein 5
B: Spindle assembly abnormal protein 5


Theoretical massNumber of molelcules
Total (without water)13,1452
Polymers13,1452
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-18 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.180, 36.290, 42.600
Angle α, β, γ (deg.)90.000, 97.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spindle assembly abnormal protein 5 / SAS-5


Mass: 6572.445 Da / Num. of mol.: 2 / Fragment: dimerization domain, UNP residues 210-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-5, F35B12.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20010
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.58 Å3/Da / Density % sol: 22.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole pH 6.4, 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.1 M carboxylic acids mixture

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→42.235 Å / Num. all: 44263 / Num. obs: 44263 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 6.78 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Rsym value: 0.108 / Net I/av σ(I): 2.588 / Net I/σ(I): 12 / Num. measured all: 305514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1-1.056.80.7630.84332363640.3140.7634.298.3
1.05-1.126.90.4341.54159460170.1770.4346.298.7
1.12-1.26.90.272.43951957300.110.278.499.2
1.2-1.296.90.23.43715653650.0820.21099.5
1.29-1.416.90.1494.63396449050.0610.14911.699.9
1.41-1.586.90.1016.63118744930.0410.10114.7100
1.58-1.836.80.0946.72692639430.0390.09417.2100
1.83-2.246.70.078.82239733650.0290.0720.6100
2.24-3.167.20.068.91881626050.0240.0624.7100
3.16-18.4867.20.0945.11063214760.0380.09426.599.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1→18.486 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1491 2232 5.04 %
Rwork0.1281 42016 -
obs0.1291 44248 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.71 Å2 / Biso mean: 11.6337 Å2 / Biso min: 2.69 Å2
Refinement stepCycle: final / Resolution: 1→18.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 124 1019
Biso mean---23.53 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071035
X-RAY DIFFRACTIONf_angle_d1.1521420
X-RAY DIFFRACTIONf_chiral_restr0.057157
X-RAY DIFFRACTIONf_plane_restr0.006201
X-RAY DIFFRACTIONf_dihedral_angle_d12.549420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.02170.18041270.18172559268698
1.0217-1.04550.20851630.15812584274798
1.0455-1.07170.15641530.13372558271198
1.0717-1.10060.1331210.12562614273599
1.1006-1.1330.14211430.11582620276399
1.133-1.16960.13271390.10952595273499
1.1696-1.21140.13741150.10722627274299
1.2114-1.25990.12481370.098326282765100
1.2599-1.31720.11891330.101726332766100
1.3172-1.38660.12281450.102526322777100
1.3866-1.47340.1351450.108726302775100
1.4734-1.58710.13331540.109226262780100
1.5871-1.74680.14581330.121926612794100
1.7468-1.99930.14971440.136126512795100
1.9993-2.51780.14511300.139826842814100
2.5178-18.48880.1731500.145127142864100

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