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- PDB-4gex: Structure of a stabilised ceSAS-6 dimer, second crystal form -

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Basic information

Entry
Database: PDB / ID: 4gex
TitleStructure of a stabilised ceSAS-6 dimer, second crystal form
ComponentsSpindle assembly abnormal protein 6
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / alpha-beta protein / centriolar / cytoplasmic / central tube
Function / homology
Function and homology information


centriole assembly / centriole replication / centrosome duplication / centriole / protein localization / regulation of cell cycle / protein domain specific binding / centrosome / identical protein binding / cytoplasm
Similarity search - Function
: / Centriolar protein SAS, helical domain / Spindle assembly abnormal protein 6, N-terminal domain / Dna Repair Protein Xrcc4; Chain: A, domain 1 / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Spindle assembly abnormal protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsErat, M.C. / Vakonakis, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Caenorhabditis elegans centriolar protein SAS-6 forms a spiral that is consistent with imparting a ninefold symmetry.
Authors: Hilbert, M. / Erat, M.C. / Hachet, V. / Guichard, P. / Blank, I.D. / Fluckiger, I. / Slater, L. / Lowe, E.D. / Hatzopoulos, G.N. / Steinmetz, M.O. / Gonczy, P. / Vakonakis, I.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindle assembly abnormal protein 6
B: Spindle assembly abnormal protein 6
C: Spindle assembly abnormal protein 6
D: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3337
Polymers78,0454
Non-polymers2883
Water32418
1
A: Spindle assembly abnormal protein 6
C: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3115
Polymers39,0232
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-35 kcal/mol
Surface area17690 Å2
MethodPISA
2
B: Spindle assembly abnormal protein 6

D: Spindle assembly abnormal protein 6


Theoretical massNumber of molelcules
Total (without water)39,0232
Polymers39,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.870, 107.870, 165.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Spindle assembly abnormal protein 6


Mass: 19511.293 Da / Num. of mol.: 4 / Fragment: N-terminal head domain / Mutation: S123E, I154W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-6, Y45F10D.9 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O62479
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 40 % (v/v) PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2012
RadiationMonochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.8→55.02 Å / Num. all: 27968 / Num. obs: 27968 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 77.96 Å2
Reflection shellResolution: 2.8→2.95 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→53.93 Å / Cor.coef. Fo:Fc: 0.9189 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1404 5.03 %RANDOM
Rwork0.2081 ---
all0.2096 27933 --
obs0.2096 27933 99.89 %-
Displacement parametersBiso mean: 81.53 Å2
Baniso -1Baniso -2Baniso -3
1--9.254 Å20 Å20 Å2
2---9.254 Å20 Å2
3---18.5081 Å2
Refine analyzeLuzzati coordinate error obs: 0.478 Å
Refinement stepCycle: LAST / Resolution: 2.8→53.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 15 18 4550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014690HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166296HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2270SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes131HARMONIC2
X-RAY DIFFRACTIONt_gen_planes634HARMONIC5
X-RAY DIFFRACTIONt_it4690HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion634SEMIHARMONIC5
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_contact4911SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2652 139 4.85 %
Rwork0.2345 2729 -
all0.236 2868 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66750.2933-0.64254.54211.542.9631-0.05430.10030.0703-0.34030.261-0.2628-0.05660.3103-0.2067-0.6491-0.11850.0204-0.5141-0.0613-0.636954.4478-28.1316-14.1572
21.4755-0.3308-0.0332.9281-0.82164.40760.0435-0.0686-0.05990.21340.12380.11470.20440.0169-0.1672-0.6167-0.01770.0688-0.69290.0615-0.588746.4897-17.276511.7046
34.0971.7714-0.84482.0245-0.9494.55510.7986-0.7985-0.3530.7901-0.6855-0.3863-0.13310.5683-0.1131-0.1842-0.3356-0.0914-0.46280-0.548339.7221-48.397810.585
410.6809-4.57164.13513.9161-1.26545.16570.91913.15771.8888-0.9588-1.4661-1.1556-0.11651.28280.547-0.41880.43020.43990.35040.7267-0.333781.7434-27.310723.0029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|168 }A3 - 168
2X-RAY DIFFRACTION2{ B|3 - B|168 }B3 - 168
3X-RAY DIFFRACTION3{ C|2 - C|167 }C2 - 167
4X-RAY DIFFRACTION4{ D|3 - D|167 }D3 - 167

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