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- PDB-4ckn: Structure of an N-terminal fragment of Leishmania SAS-6 containin... -

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Basic information

Entry
Database: PDB / ID: 4ckn
TitleStructure of an N-terminal fragment of Leishmania SAS-6 containing parts of its coiled coil domain, F257E mutant
ComponentsSAS-6
KeywordsSTRUCTURAL PROTEIN / BASAL BODY / CENTRIOLE / CARTWHEEL / TRYPANOSOMATIDS
Function / homology
Function and homology information


centriole replication / centriole / ciliary basal body / cytoplasm
Similarity search - Function
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 N-terminal domain-containing protein
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
Authorsvan Breugel, M.
CitationJournal: Elife / Year: 2014
Title: Structure of the SAS-6 cartwheel hub from Leishmania major.
Authors: van Breugel, M. / Wilcken, R. / McLaughlin, S.H. / Rutherford, T.J. / Johnson, C.M.
History
DepositionJan 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAS-6
B: SAS-6
C: SAS-6
D: SAS-6


Theoretical massNumber of molelcules
Total (without water)99,6734
Polymers99,6734
Non-polymers00
Water00
1
A: SAS-6
B: SAS-6


Theoretical massNumber of molelcules
Total (without water)49,8362
Polymers49,8362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-25.6 kcal/mol
Surface area20610 Å2
MethodPISA
2
C: SAS-6
D: SAS-6


Theoretical massNumber of molelcules
Total (without water)49,8362
Polymers49,8362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-25.9 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.855, 81.253, 133.149
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
12C
22D
13C
23A
14B
24D
15B
25A
16D
26A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALACC130 - 31336 - 219
21GLUGLUALAALABB130 - 31336 - 219
12PROPROASNASNCC131 - 31537 - 221
22PROPROASNASNDD131 - 31537 - 221
13PROPROALAALACC131 - 31337 - 219
23PROPROALAALAAA131 - 31337 - 219
14PROPROALAALABB131 - 31437 - 220
24PROPROALAALADD131 - 31437 - 220
15PROPROALAALABB131 - 31437 - 220
25PROPROALAALAAA131 - 31437 - 220
16PROPROALAALADD131 - 31437 - 220
26PROPROALAALAAA131 - 31437 - 220

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.4152, -0.776, 0.4748), (-0.8267, 0.1041, -0.5529), (0.3796, -0.6221, -0.6847)-36.12, -7.008, 36.66
2given(-0.1199, -0.6629, 0.7391), (-0.65, -0.5103, -0.5631), (0.7504, -0.5479, -0.3697)-67.11, -83.93, 7.846
3given(0.8237, -0.5083, -0.2511), (0.5662, 0.7605, 0.3178), (0.02943, -0.404, 0.9143)-28.05, -76.77, -31.71

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Components

#1: Protein
SAS-6


Mass: 24918.141 Da / Num. of mol.: 4
Fragment: N-TERMINAL DOMAIN AND PARTS OF THE COILED COIL DOMAIN, RESIDUES 97-320
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Description: SYNTHETIC GENE / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E9AFQ5
Sequence detailsTHE CRYSTALLISED CONSTRUCT CONTAINS THE F257E MUTATION TO WEAKEN DIMERISATION OF THE N-TERMINAL DOMAIN.

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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: 2.89 Å3/Da / Density % sol: 57.52 % / Description: NONE
Crystal growpH: 5.85 / Details: 100 MM NACITRATE PH 5.85, 21% (W/V) PEG-3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→46.91 Å / Num. obs: 25904 / % possible obs: 99.9 % / Observed criterion σ(I): 0.9 / Redundancy: 7.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0047refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CKM

4ckm


Resolution: 2.9→133.1 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 22.834 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R: 1.376 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25597 1279 5 %RANDOM
Rwork0.23673 ---
obs0.23775 24090 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.751 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å2-4.49 Å2
2---1.04 Å20 Å2
3---4.49 Å2
Refinement stepCycle: LAST / Resolution: 2.9→133.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5653 0 0 0 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195759
X-RAY DIFFRACTIONr_bond_other_d0.0050.025544
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9767802
X-RAY DIFFRACTIONr_angle_other_deg1.172312704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50423.298285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63415977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151556
X-RAY DIFFRACTIONr_chiral_restr0.0640.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216484
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021342
X-RAY DIFFRACTIONr_nbd_refined0.2350.21021
X-RAY DIFFRACTIONr_nbd_other0.1840.25227
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22804
X-RAY DIFFRACTIONr_nbtor_other0.0880.23571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.110.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4290.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4779.1242835
X-RAY DIFFRACTIONr_mcbond_other4.4749.1222834
X-RAY DIFFRACTIONr_mcangle_it7.41813.6693528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5659.5162924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.56214.1164274
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C101330.11
12B101330.11
21C91090.15
22D91090.15
31C98240.13
32A98240.13
41B89670.15
42D89670.15
51B98260.13
52A98260.13
61D88770.16
62A88770.16
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 66 -
Rwork0.409 1510 -
obs--83.47 %

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