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- PDB-4ckp: Structure of an N-terminal fragment of Leishmania SAS-6 that cont... -

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Basic information

Entry
Database: PDB / ID: 4ckp
TitleStructure of an N-terminal fragment of Leishmania SAS-6 that contains part of its coiled coil domain
ComponentsSAS-6
KeywordsSTRUCTURAL PROTEIN / BASAL BODY / CENTRIOLE / CARTWHEEL / TRYPANOSOMATIDS
Function / homology
Function and homology information


centriole replication / centriole / ciliary basal body / centrosome / 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: 3.45 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 1.3Apr 19, 2017Group: Data collection
Revision 1.4Jan 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 1.5Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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. THE SHEETS PRESENTED AS "EA" 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 "FA" 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
E: SAS-6
F: SAS-6


Theoretical massNumber of molelcules
Total (without water)149,6176
Polymers149,6176
Non-polymers00
Water00
1
A: SAS-6
B: SAS-6
C: SAS-6
D: SAS-6
E: SAS-6
F: SAS-6

A: SAS-6
B: SAS-6
C: SAS-6
D: SAS-6
E: SAS-6
F: SAS-6

A: SAS-6
B: SAS-6
C: SAS-6
D: SAS-6
E: SAS-6
F: SAS-6


Theoretical massNumber of molelcules
Total (without water)448,85218
Polymers448,85218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area40150 Å2
ΔGint-315.1 kcal/mol
Surface area175790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)482.681, 482.681, 43.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4989, 0.8666, -0.005611), (0.8666, 0.499, 0.003026), (0.005421, -0.003353, -1)-6.738, 3.591, 33.59
2given(0.7653, -0.6429, -0.03131), (0.6412, 0.7658, -0.04945), (0.05576, 0.01777, 0.9983)1.782, 3.134, 6.539
3given(0.2296, 0.973, -0.02508), (0.9728, -0.2302, -0.02704), (-0.03208, -0.01819, -0.9993)0.5291, 3.637, 29.57
4given(0.1343, -0.9909, -0.00725), (0.9906, 0.1345, -0.02694), (0.02767, -0.003563, 0.9996)-3.532, 4.378, 3.434
5given(0.8197, 0.5728, 0.003394), (0.5728, -0.8196, -0.01106), (-0.00355, 0.01101, -0.9999)2.735, -0.04475, 32.28

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Components

#1: Protein
SAS-6


Mass: 24936.201 Da / Num. of mol.: 6
Fragment: N-TERMINAL DOMAIN AND PART OF THE COILED COIL DOMAIN, RESIDUES 97-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E9AFQ5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 6.34 Å3/Da / Density % sol: 80.61 % / Description: NONE
Crystal growpH: 6.23
Details: 100 MM BISTRIS PH 6.23, 100 MM NAACETATE (NOT PH ADJUSTED), 26.5-27% (W/V) PEG-400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97813
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97813 Å / Relative weight: 1
ReflectionResolution: 3.45→66.94 Å / Num. obs: 49349 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 22.3 % / Biso Wilson estimate: 98.41 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 8.2
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CKM

4ckm


Resolution: 3.45→42.901 Å / SU ML: 0.54 / σ(F): 0.23 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 4865 5.1 %
Rwork0.2239 --
obs0.2248 48521 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 150 Å2
Refinement stepCycle: LAST / Resolution: 3.45→42.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8777 0 0 0 8777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068951
X-RAY DIFFRACTIONf_angle_d1.34812146
X-RAY DIFFRACTIONf_dihedral_angle_d14.5683322
X-RAY DIFFRACTIONf_chiral_restr0.0511385
X-RAY DIFFRACTIONf_plane_restr0.0051600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4501-3.48920.44591220.3992342X-RAY DIFFRACTION74
3.4892-3.53030.38871480.38682609X-RAY DIFFRACTION83
3.5303-3.57330.3691320.3682841X-RAY DIFFRACTION88
3.5733-3.61850.32871480.38392890X-RAY DIFFRACTION93
3.6185-3.66610.3611650.37572962X-RAY DIFFRACTION98
3.6661-3.71630.42581560.37283059X-RAY DIFFRACTION99
3.7163-3.76940.39951810.333103X-RAY DIFFRACTION100
3.7694-3.82560.34081620.3153169X-RAY DIFFRACTION100
3.8256-3.88530.34821960.32453155X-RAY DIFFRACTION99
3.8853-3.9490.36951600.33483176X-RAY DIFFRACTION100
3.949-4.0170.39181280.312966X-RAY DIFFRACTION100
4.017-4.090.33112140.2863030X-RAY DIFFRACTION100
4.09-4.16860.26711620.27033160X-RAY DIFFRACTION100
4.1686-4.25360.28621860.26533173X-RAY DIFFRACTION100
4.2536-4.34610.22741760.24523124X-RAY DIFFRACTION99
4.3461-4.4470.24651640.24963024X-RAY DIFFRACTION100
4.447-4.55810.2581580.22413108X-RAY DIFFRACTION100
4.5581-4.68120.18012070.20033106X-RAY DIFFRACTION99
4.6812-4.81880.19931580.1943133X-RAY DIFFRACTION98
4.8188-4.97410.24231300.21553046X-RAY DIFFRACTION100
4.9741-5.15160.22431580.21693122X-RAY DIFFRACTION100
5.1516-5.35750.24381540.19853230X-RAY DIFFRACTION100
5.3575-5.60090.23251780.2263016X-RAY DIFFRACTION100
5.6009-5.89540.241560.21113118X-RAY DIFFRACTION100
5.8954-6.26380.21731480.1873226X-RAY DIFFRACTION100
6.2638-6.74570.19071160.2013072X-RAY DIFFRACTION100
6.7457-7.42140.24971780.19273148X-RAY DIFFRACTION100
7.4214-8.4880.17861720.16363148X-RAY DIFFRACTION100
8.488-10.66680.19031740.16283094X-RAY DIFFRACTION100
10.6668-42.90420.15581780.13783063X-RAY DIFFRACTION99
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)
16.1176-1.64070.58755.1458-1.11675.3926-0.13480.1786-0.26460.13080.06690.1744-0.9571.1279-0.00071.01310.27270.00792.07610.06590.718-36.6095-99.706414.2528
26.2483-1.35780.89073.8853-0.81114.5076-0.3003-0.2524-0.22630.40610.16160.2927-0.92470.03630.10121.83010.70230.05811.15010.00720.6251-74.7911-77.349419.2034
33.8745-0.03941.45295.5874-1.62665.9268-0.09550.0029-0.14870.49780.11080.24110.25770.8885-0.04861.47520.52290.27121.02890.0740.6109-94.8055-54.107513.8347
44.0151-0.72610.73265.6836-2.84493.813-0.0037-0.0367-0.12070.3956-0.21220.4472-0.55720.7090.13792.5270.13570.02410.8007-0.01470.7317-108.5419-11.862818.8032
53.70761.9089-0.96545.5282-1.99374.42980.0828-0.05990.0717-0.2085-0.17960.27560.56970.8310.05232.52420.12490.04780.7585-0.01810.7206-107.242918.550414.0066
63.90540.7902-0.86166.0342-1.37183.3820.2506-0.41550.12270.0642-0.08910.14310.34830.8041-0.17121.8061-0.6069-0.0941.47280.09860.7196-89.074159.078618.881
72.95040.68521.647.80830.62612.8179-0.05751.5206-1.2231-2.00230.74361.0971-0.02360.2637-0.57241.36710.6867-0.32552.41420.00931.5246-62.4945-100.620113.097
83.1438-0.9496-1.99132.9552-0.79192.35130.5299-1.0802-1.80371.9502-0.2275-0.0826-0.5373-0.7596-0.22491.37980.6844-0.19221.95710.35791.5126-62.4923-101.254320.3393
95.85951.47570.04960.94580.33953.6394-0.07011.35420.4092-0.20970.25211.1730.179-1.2988-0.16861.31650.58120.04111.2970.15931.5734-124.6557-38.577116.0593
102.97130.9603-1.39312.9386-1.08972.58620.701-1.59810.27760.1502-0.27211.329-0.2896-1.0755-0.25351.580.30410.12521.24130.23951.4213-123.6774-40.935321.6167
113.9952-3.28540.81341.1709-0.14180.0478-0.15020.6172-0.33420.0429-0.03050.34680.5725-0.42360.21142.0485-0.16950.06821.05560.18341.1006-120.961350.308313.7764
128.6425-2.8371-1.03251.2740.6311.5986-0.3619-1.80860.54140.92190.26660.19990.1490.0040.02722.1387-0.27420.24741.0565-0.04751.0217-120.720347.30319.5064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 129:271
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 129:271
3X-RAY DIFFRACTION3CHAIN C AND RESSEQ 129:271
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 130:271
5X-RAY DIFFRACTION5CHAIN E AND RESSEQ 130:271
6X-RAY DIFFRACTION6CHAIN F AND RESSEQ 130:271
7X-RAY DIFFRACTION7CHAIN A AND RESSEQ 272:304
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 272:305
9X-RAY DIFFRACTION9CHAIN C AND RESSEQ 272:317
10X-RAY DIFFRACTION10CHAIN D AND RESSEQ 272:317
11X-RAY DIFFRACTION11CHAIN E AND RESSEQ 272:319
12X-RAY DIFFRACTION12CHAIN F AND RESSEQ 272:318

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