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- PDB-5al7: N-terminal fragment of Drosophila melanogaster Sas-6 (F143D), dim... -

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Basic information

Entry
Database: PDB / ID: 5al7
TitleN-terminal fragment of Drosophila melanogaster Sas-6 (F143D), dimerised via the coiled-coil domain.
ComponentsSPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
KeywordsSTRUCTURAL PROTEIN / CENTRIOLE / CARTWHEEL
Function / homology
Function and homology information


ciliary basal body organization / centriole assembly / centriole-centriole cohesion / centrosome cycle / centriole replication / centrosome duplication / centriole / ciliary basal body / centrosome / cytoplasm
Similarity search - Function
Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal
Similarity search - Domain/homology
NITRATE ION / Spindle assembly abnormal protein 6 homolog
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsCottee, M.A. / Johnson, S. / Lea, S.M.
CitationJournal: Elife / Year: 2015
Title: The homo-oligomerisation of both Sas-6 and Ana2 is required for efficient centriole assembly in flies.
Authors: Cottee, M.A. / Muschalik, N. / Johnson, S. / Leveson, J. / Raff, J.W. / Lea, S.M.
History
DepositionMar 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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.

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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 HOMOLOG
B: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4614
Polymers50,3372
Non-polymers1242
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21.5 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 64.740, 123.730
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.016, 0.003), (-0.016, -0.999, 0.038), (0.004, 0.038, 0.999)46.614, 35.138, -1.377
2given(-1, -0.016, 0.004), (0.016, -0.999, 0.038), (0.003, 0.038, 0.999)47.174, 34.41, -0.128

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Components

#1: Protein SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG / SAS-6


Mass: 25168.453 Da / Num. of mol.: 2
Fragment: N-TERMINAL HEAD GROUP PLUS COILED-COIL, UNP RESIDUES 2-216
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETM-14 / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): B834 (DE3) / References: UniProt: Q9VAC8
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAAL68137 VARIANT, E36D, I207L

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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: 3.74 Å3/Da / Density % sol: 67.09 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M BICINE/TRIZMA MIX (PH 8.5), 20% W/V PEG 550MME, 10% W/V PEG 20K, 30 MM NANO3, 30 MM NA2HPO4, 30 MM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorDate: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.92→41.43 Å / Num. obs: 15767 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 43.17 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.1
Reflection shellResolution: 2.92→3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF PDB ENTRIES 2Y3V A,B,D, 2Y3W A, B 3Q0X A,B

2y3v

2y3w

3q0x


Resolution: 2.92→41.429 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 788 5 %
Rwork0.1832 --
obs0.1847 15764 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→41.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 8 33 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073414
X-RAY DIFFRACTIONf_angle_d1.0554592
X-RAY DIFFRACTIONf_dihedral_angle_d15.6331314
X-RAY DIFFRACTIONf_chiral_restr0.044520
X-RAY DIFFRACTIONf_plane_restr0.005600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9202-3.10310.3191540.25052456X-RAY DIFFRACTION98
3.1031-3.34260.25341020.21192535X-RAY DIFFRACTION98
3.3426-3.67880.22961330.18552492X-RAY DIFFRACTION98
3.6788-4.21060.2081410.16182497X-RAY DIFFRACTION98
4.2106-5.30320.17171210.14952500X-RAY DIFFRACTION97
5.3032-41.43350.19671370.19482496X-RAY DIFFRACTION95
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)
14.1636-0.0043-0.7352.06080.05931.69680.2377-0.03990.1628-0.0311-0.09850.11270.0919-0.1873-0.14450.2756-0.04620.00820.26520.01860.211713.134131.2552-16.1548
22.5286-0.58210.03274.51730.80861.49020.0127-0.14410.1349-0.18060.01460.26410.1215-0.09190.0010.2386-0.0581-0.01350.28490.03190.206713.775433.6998-17.1789
30.3778-0.13130.00590.0498-0.01290.0025-0.24910.47040.41410.0580.17250.04420.12880.37260.07082.40660.107-0.27462.53950.16771.448826.717911.6815-70.7963
43.75620.10470.1423.4056-0.88371.64520.0389-0.135-0.2078-0.1762-0.0558-0.3247-0.02050.22290.01260.2432-0.05820.00520.28490.00460.220335.54380.4934-17.0156
51.17270.08480.25641.6475-1.68351.80620.1537-0.4846-0.26090.4446-0.0473-0.4676-0.242-0.0417-0.05120.2808-0.075-0.02490.3783-0.02110.316732.4245-6.5887-7.9655
61.39510.1280.9470.5765-0.12556.27630.11650.83080.1925-0.8871-0.2511-0.1867-0.94870.1015-0.070.98350.10930.0580.6743-0.01360.403726.497119.5758-34.2229
71.01520.03140.03830.82840.04051.1223-0.0784-0.61830.1458-1.00080.2749-0.12260.6672-0.3318-0.17432.63040.1668-0.35452.3057-0.16231.218719.924415.719-77.7645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 87 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 88 THROUGH 184 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 185 THROUGH 216 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 119 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 120 THROUGH 157 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 158 THROUGH 193 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 194 THROUGH 216 )

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