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- PDB-5oi9: Trichoplax adhaerens STIL N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5oi9
TitleTrichoplax adhaerens STIL N-terminal domain
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / Centrosomes / centriole / STIL / CEP85
Function / homologySCL-interrupting locus protein / SCL-interrupting locus protein N-terminus / protein localization to centrosome / smoothened signaling pathway / centrosome duplication / centriole / mitotic spindle organization / centrosome / Uncharacterized protein
Function and homology information
Biological speciesTrichoplax adhaerens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
Authorsvan Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly.
Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. ...Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. / Raught, B. / Pelletier, L. / van Breugel, M.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5183
Polymers81,3232
Non-polymers1951
Water5,296294
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)40,6611
Polymers40,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8572
Polymers40,6611
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 75.231, 68.530
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 40661.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: TRIADDRAFT_58880 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: B3S3X5
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.0 3 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87292 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87292 Å / Relative weight: 1
ReflectionResolution: 2.09→37.62 Å / Num. obs: 39751 / % possible obs: 100 % / Redundancy: 5.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2 / Num. unique obs: 3077 / CC1/2: 0.592 / Rpim(I) all: 0.416 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
CRANKphasing
RefinementMethod to determine structure: MAD / Resolution: 2.09→37.615 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2408 3844 4.94 %
Rwork0.197 --
obs0.1991 39724 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→37.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 12 294 5530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035372
X-RAY DIFFRACTIONf_angle_d0.5737300
X-RAY DIFFRACTIONf_dihedral_angle_d10.3073267
X-RAY DIFFRACTIONf_chiral_restr0.047850
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.086-2.11240.36491380.29972701X-RAY DIFFRACTION100
2.1124-2.14020.32761440.2812778X-RAY DIFFRACTION100
2.1402-2.16950.30031680.28112712X-RAY DIFFRACTION100
2.1695-2.20050.31431780.26072713X-RAY DIFFRACTION100
2.2005-2.23340.27571540.2582685X-RAY DIFFRACTION100
2.2334-2.26830.28961620.25332770X-RAY DIFFRACTION100
2.2683-2.30550.32091620.25182659X-RAY DIFFRACTION100
2.3055-2.34520.29231440.25222775X-RAY DIFFRACTION100
2.3452-2.38780.30331650.24232709X-RAY DIFFRACTION100
2.3878-2.43380.26421340.23722760X-RAY DIFFRACTION100
2.4338-2.48340.29851430.2312736X-RAY DIFFRACTION100
2.4834-2.53740.25261190.22452805X-RAY DIFFRACTION100
2.5374-2.59640.25661600.22352646X-RAY DIFFRACTION100
2.5964-2.66130.24741430.21892758X-RAY DIFFRACTION100
2.6613-2.73330.32471600.21082732X-RAY DIFFRACTION100
2.7333-2.81370.22951120.21022755X-RAY DIFFRACTION100
2.8137-2.90450.29391380.20842784X-RAY DIFFRACTION100
2.9045-3.00820.2471330.19192758X-RAY DIFFRACTION100
3.0082-3.12860.1868950.17822795X-RAY DIFFRACTION100
3.1286-3.27090.22431100.18072789X-RAY DIFFRACTION100
3.2709-3.44330.23591280.17142746X-RAY DIFFRACTION100
3.4433-3.65880.23121330.15942721X-RAY DIFFRACTION100
3.6588-3.94110.21341550.16132728X-RAY DIFFRACTION100
3.9411-4.33720.1661210.15592789X-RAY DIFFRACTION100
4.3372-4.96350.15581280.14512743X-RAY DIFFRACTION100
4.9635-6.24890.23921850.18072715X-RAY DIFFRACTION100
6.2489-37.62150.17831320.1792733X-RAY DIFFRACTION100

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