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- PDB-6z4a: Structure of the human SAS-6 N-terminal domain, F131E mutant -

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Basic information

Entry
Database: PDB / ID: 6z4a
TitleStructure of the human SAS-6 N-terminal domain, F131E mutant
ComponentsSpindle assembly abnormal protein 6 homolog
KeywordsSTRUCTURAL PROTEIN / centrosome / centriole / cartwheel / alpha/beta protein
Function / homology
Function and homology information


deuterosome / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / centriole / centrosome / cytoplasm
Similarity search - Function
SAS-6 coiled-coil domain / Sas6/XLF/XRCC4 coiled-coil domain / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain
Similarity search - Domain/homology
Spindle assembly abnormal protein 6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBusch, J.M.C. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Identification of compounds that bind the centriolar protein SAS-6 and inhibit its oligomerization.
Authors: Busch, J.M.C. / Matsoukas, M.T. / Musgaard, M. / Spyroulias, G.A. / Biggin, P.C. / Vakonakis, I.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindle assembly abnormal protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8382
Polymers17,7461
Non-polymers921
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 65.130, 38.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Spindle assembly abnormal protein 6 homolog / HsSAS-6


Mass: 17745.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SASS6, SAS6 / Plasmid: pFLOAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6UVJ0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES 30% w/v PEG 6000 Cryoprotected by addition of 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→21.98 Å / Num. obs: 26380 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.027 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1273 / CC1/2: 0.566 / Rpim(I) all: 0.526 / Rrim(I) all: 1.238 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y3V

2y3v


Resolution: 1.46→21.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1247 4.73 %RANDOM
Rwork0.199 ---
obs0.201 26340 99.7 %-
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.3263 Å20 Å20 Å2
2---1.4837 Å20 Å2
3----0.8426 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.46→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 6 93 1318
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092569HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14678HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d578SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it2569HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion14.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion167SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2721SEMIHARMONIC4
LS refinement shellResolution: 1.46→1.47 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3472 -4.93 %
Rwork0.2935 501 -
all0.2961 527 -
obs--99.62 %
Refinement TLS params.Method: refined / Origin x: 10.967 Å / Origin y: 74.0722 Å / Origin z: 13.6684 Å
111213212223313233
T-0.0097 Å2-0.0012 Å2-0.0017 Å2--0.0213 Å20.0132 Å2---0.012 Å2
L1.2382 °2-0.0377 °20.3993 °2-0.2747 °2-0.1295 °2--0 °2
S0.008 Å °0.033 Å °-0.0302 Å °-0.0068 Å °-0.0075 Å °0.028 Å °0.0001 Å °0.0161 Å °-0.0005 Å °
Refinement TLS groupSelection details: { A|* }

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