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- PDB-5lhw: Central Coiled-Coil Domain of Human STIL -

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Basic information

Entry
Database: PDB / ID: 5lhw
TitleCentral Coiled-Coil Domain of Human STIL
ComponentsSCL-interrupting locus protein
KeywordsSTRUCTURAL PROTEIN / Centriole
Function / homology
Function and homology information


floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / positive regulation of spindle assembly / notochord development / determination of left/right symmetry / protein localization to centrosome / neural tube development ...floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / positive regulation of spindle assembly / notochord development / determination of left/right symmetry / protein localization to centrosome / neural tube development / smoothened signaling pathway / heart looping / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / forebrain development / centriole / mitotic spindle organization / neural tube closure / multicellular organism growth / cell cortex / in utero embryonic development / centrosome / negative regulation of apoptotic process / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus
Similarity search - Domain/homology
SCL-interrupting locus protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å
AuthorsCottee, M.A. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust104575 United Kingdom
CitationJournal: Biol Open / Year: 2017
Title: A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies.
Authors: Cottee, M.A. / Johnson, S. / Raff, J.W. / Lea, S.M.
History
DepositionJul 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: 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: SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4822
Polymers3,2001
Non-polymers2821
Water28816
1
A: SCL-interrupting locus protein
hetero molecules

A: SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9644
Polymers6,3992
Non-polymers5652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area1410 Å2
ΔGint-12 kcal/mol
Surface area4880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.310, 40.310, 29.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

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Components

#1: Protein/peptide SCL-interrupting locus protein / TAL-1-interrupting locus protein


Mass: 3199.662 Da / Num. of mol.: 1 / Fragment: UNP residues 726-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIL, SIL / Production host: Escherichia coli B (bacteria) / Strain (production host): C41 / References: UniProt: Q15468
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.86 Å3/Da / Density % sol: 33.71 % / Description: Large Block
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 150 nl protein solution (58.6 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM TCEP) and 150 nl of mother liquor (7 mM HEPES pH 8.2, 93 mM Tris pH 9.0, 55.36% v/v PEG 550 MME, 10% v/v glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.91→23.663 Å / Num. obs: 17643 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC1/2: 0.996 / Net I/σ(I): 24
Reflection shellHighest resolution: 0.91 Å / Rmerge(I) obs: 0.668

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PolyAla helix based on 5AL6

5al6


Resolution: 0.91→23.663 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.67
RfactorNum. reflection% reflection
Rfree0.1387 896 5.08 %
Rwork0.1345 --
obs0.1347 17638 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.91→23.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms221 0 19 16 256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02256
X-RAY DIFFRACTIONf_angle_d1.607337
X-RAY DIFFRACTIONf_dihedral_angle_d16.303112
X-RAY DIFFRACTIONf_chiral_restr0.10637
X-RAY DIFFRACTIONf_plane_restr0.00944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9101-0.96720.24811380.19352630X-RAY DIFFRACTION95
0.9672-1.04180.1431640.12912724X-RAY DIFFRACTION99
1.0418-1.14670.10031290.09922799X-RAY DIFFRACTION100
1.1467-1.31260.11541610.09032783X-RAY DIFFRACTION100
1.3126-1.65370.11471520.11172825X-RAY DIFFRACTION100
1.6537-23.67140.15081520.15062981X-RAY DIFFRACTION99

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