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- PDB-3pyi: Structure of the N-terminal domain of C. elegans SAS-6 -

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Basic information

Entry
Database: PDB / ID: 3pyi
TitleStructure of the N-terminal domain of C. elegans SAS-6
ComponentsSpindle assembly abnormal protein 6
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / dimer / alpha-beta protein / cytoplasmic / centriolar
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 / SAD / Resolution: 2.104 Å
AuthorsVakonakis, I. / Steinmetz, M.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis of the 9-fold symmetry of centrioles.
Authors: Kitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Fluckiger, I. / Gonczy, P. / Steinmetz, M.O.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,8497
Polymers38,8762
Non-polymers9725
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-5 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.273, 73.153, 79.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and not (resid 18:27 or resid 58:62 or...
211chain B and not (resid 18:27 or resid 58:62 or...

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Components

#1: Protein Spindle assembly abnormal protein 6


Mass: 19438.242 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 1-168 / Mutation: S123E
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% v/v PEG200, 5% w/v PEG3000, 0.1 M MES, seeding with crushed original crystals, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2010
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.104→73.153 Å / Num. all: 24437 / Num. obs: 24368 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.25 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.7
Reflection shellResolution: 2.104→2.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4 / Num. unique all: 3498 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.6_289)refinement
XSCALEdata scaling
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.104→50.678 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic with TLS restraints / σ(F): 1.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2220 4.94 %Random
Rwork0.2101 ---
obs0.2124 23106 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.464 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.83 Å2
Baniso -1Baniso -2Baniso -3
1-14.0832 Å2-0 Å2-0 Å2
2---11.7579 Å2-0 Å2
3----2.3252 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.104→50.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 49 146 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072445
X-RAY DIFFRACTIONf_angle_d1.0233285
X-RAY DIFFRACTIONf_dihedral_angle_d16.866955
X-RAY DIFFRACTIONf_chiral_restr0.072380
X-RAY DIFFRACTIONf_plane_restr0.004410
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A925X-RAY DIFFRACTIONPOSITIONAL
12B925X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1039-2.17910.34512280.28494223446497
2.1791-2.26630.31512200.26294304453398
2.2663-2.36950.28292240.23794306455198
2.3695-2.49440.2712240.22284285451598
2.4944-2.65070.31722250.21024318454998
2.6507-2.85530.28042200.21594299453099
2.8553-3.14260.26552220.224292451998
3.1426-3.59720.28612230.20944294451998
3.5972-4.53170.19882160.17574216443397
4.5317-50.69280.2052180.18324224445196
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)
10.249-0.1020.24642.93240.7521.68260.0321-0.0191-0.0460.14990.034-0.07340.0768-0.0275-0.06180.1255-0.01110.02680.18230.00620.18921.0494-9.290416.1836
20.7640.0706-0.20482.2110.26861.46140.10110.08430.1344-0.35690.0514-0.2524-0.23580.1155-0.13250.291-0.00670.00790.18160.00230.240.4763-2.1058-15.7368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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