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- PDB-4gfc: N-terminal coiled-coil dimer of C.elegans SAS-6, crystal form B -

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Basic information

Entry
Database: PDB / ID: 4gfc
TitleN-terminal coiled-coil dimer of C.elegans SAS-6, crystal form B
ComponentsSpindle assembly abnormal protein 6
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / alpha-beta protein / cytoplasmic / centriolar / 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
IMIDAZOLE / Spindle assembly abnormal protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 3, 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
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 28, 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
A: Spindle assembly abnormal protein 6
B: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,07314
Polymers43,0502
Non-polymers1,02312
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint6 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.520, 50.720, 101.870
Angle α, β, γ (deg.)90.00, 97.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spindle assembly abnormal protein 6


Mass: 21524.752 Da / Num. of mol.: 2
Fragment: SAS-6 N-terminal head domain and beginning of coiled coil
Mutation: I154G
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 20,000, 20% PEG MME 550, 0.1M MES/Imidazole buffer pH 6.5 and 0.02M of each of these monosaccharides (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine), ...Details: 10% PEG 20,000, 20% PEG MME 550, 0.1M MES/Imidazole buffer pH 6.5 and 0.02M of each of these monosaccharides (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→51.27 Å / Num. all: 12487 / Num. obs: 12487 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 94.56 Å2
Reflection shellResolution: 2.85→3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→51.27 Å / Cor.coef. Fo:Fc: 0.9076 / Cor.coef. Fo:Fc free: 0.9004 / SU R Cruickshank DPI: 0.72 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 601 4.81 %RANDOM
Rwork0.2145 ---
all0.2155 12487 --
obs0.2155 12487 99.95 %-
Displacement parametersBiso mean: 124.88 Å2
Baniso -1Baniso -2Baniso -3
1-20.2207 Å20 Å21.849 Å2
2---9.5407 Å20 Å2
3----10.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: LAST / Resolution: 2.85→51.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 53 38 2646
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012635HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1279SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes366HARMONIC5
X-RAY DIFFRACTIONt_it2635HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion3.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
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_contact2781SEMIHARMONIC4
LS refinement shellResolution: 2.85→3.12 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3038 133 4.54 %
Rwork0.2108 2799 -
all0.2147 2932 -
obs--99.95 %
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)
16.0805-0.0498-1.23562.9236-0.18111.86970.03440.3542-0.12190.0744-0.05110.057-0.1225-0.01510.0167-0.6637-0.0334-0.0492-1.001-0.0757-0.381-24.3904-7.520844.9744
211.63872.5713-4.42421.9829-2.291512.0453-0.18334.6460.3359-0.6572-0.1202-0.507-0.10450.65040.3035-0.90420.18250.13510.93560.2438-0.73993.1101-7.113720.0228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|44 A|48 - A|162 A|164 - A|170 }A2 - 44
2X-RAY DIFFRACTION1{ A|2 - A|44 A|48 - A|162 A|164 - A|170 }A48 - 162
3X-RAY DIFFRACTION1{ A|2 - A|44 A|48 - A|162 A|164 - A|170 }A164 - 170
4X-RAY DIFFRACTION2{ B|3 - B|19 B|28 - B|44 B|51 - B|118 B|134 - B|163 }B3 - 19
5X-RAY DIFFRACTION2{ B|3 - B|19 B|28 - B|44 B|51 - B|118 B|134 - B|163 }B28 - 44
6X-RAY DIFFRACTION2{ B|3 - B|19 B|28 - B|44 B|51 - B|118 B|134 - B|163 }B51 - 118
7X-RAY DIFFRACTION2{ B|3 - B|19 B|28 - B|44 B|51 - B|118 B|134 - B|163 }B134 - 163

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