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

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Basic information

Entry
Database: PDB / ID: 4gfa
TitleN-terminal coiled-coil dimer of C.elegans SAS-6, crystal form A
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
Spindle assembly abnormal protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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 1.3Jun 21, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Spindle assembly abnormal protein 6
D: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8145
Polymers83,6964
Non-polymers1181
Water00
1
A: Spindle assembly abnormal protein 6
C: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9663
Polymers41,8482
Non-polymers1181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-24 kcal/mol
Surface area18010 Å2
MethodPISA
2
B: Spindle assembly abnormal protein 6
D: Spindle assembly abnormal protein 6


Theoretical massNumber of molelcules
Total (without water)41,8482
Polymers41,8482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-17 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.150, 118.940, 121.870
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


Mass: 20924.043 Da / Num. of mol.: 4 / Fragment: N-terminal coiled coil
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M LiSO4, 0.1M MES pH6, 35% MPD, 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: 3.55→85.12 Å / Num. all: 13307 / Num. obs: 13307 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 63.37 Å2
Reflection shellResolution: 3.55→3.74 Å / % possible all: 99.9

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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: 3.55→62.31 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.8003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3574 660 4.97 %RANDOM
Rwork0.3099 ---
all0.3122 13285 --
obs0.3122 13285 99.1 %-
Displacement parametersBiso mean: 100.97 Å2
Baniso -1Baniso -2Baniso -3
1--5.4376 Å20 Å20 Å2
2--6.8747 Å20 Å2
3----1.4371 Å2
Refine analyzeLuzzati coordinate error obs: 1.116 Å
Refinement stepCycle: LAST / Resolution: 3.55→62.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 8 0 4958
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.186784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2438SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes701HARMONIC5
X-RAY DIFFRACTIONt_it5046HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion3.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion682SEMIHARMONIC5
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_contact5446SEMIHARMONIC4
LS refinement shellResolution: 3.55→3.83 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3112 129 4.78 %
Rwork0.2487 2567 -
all0.2519 2696 -
obs--99.1 %
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)
15.8240.02490.7944.5850.83453.35720.2279-0.26150.39240.6556-0.1439-0.1109-0.33470.2057-0.084-0.1230.1060.2012-0.2512-0.0559-0.050332.370917.876710.8429
24.0511-1.235-2.00663.14921.06243.88250.5652-0.03560.2827-0.4555-0.45040.2434-0.4839-0.082-0.1149-0.0307-0.11850.2814-0.09630.05310.169840.978320.716349.7016
35.60470.3890.35667.52910.02382.2736-0.12590.5674-0.0387-1.47850.13690.1456-0.195-0.3736-0.0109-0.0914-0.07710.0059-0.20290.0105-0.200513.3703-7.2289-10.7496
43.1904-1.0071-1.60983.32492.15350.36050.0502-0.24320.26270.8522-0.0869-0.46220.0960.57740.0367-0.02140.0240.12570.23360.0432-0.076159.9272-4.371171.2418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|157 }A3 - 157
2X-RAY DIFFRACTION2{ B|3 - B|157 }B3 - 157
3X-RAY DIFFRACTION3{ C|4 - C|156 }C4 - 156
4X-RAY DIFFRACTION4{ D|5 - D|41 D|48 - D|156 }D5 - 41
5X-RAY DIFFRACTION4{ D|5 - D|41 D|48 - D|156 }D48 - 156

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