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- PDB-2y3v: N-terminal head domain of Danio rerio SAS-6 -

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Basic information

Entry
Database: PDB / ID: 2y3v
TitleN-terminal head domain of Danio rerio SAS-6
ComponentsSPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / BASAL BODY / CENTRIOLE / CARTWHEEL / CARTWHEEL HUB
Function / homology
Function and homology information


positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle ...positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / centriole / mitotic spindle organization / spermatogenesis / centrosome / cytoplasm
Similarity search - Function
SAS-6 coiled-coil domain / Sas6/XLF/XRCC4 coiled-coil 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 homolog
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
Authorsvan Breugel, M.
CitationJournal: Science / Year: 2011
Title: Structures of SAS-6 suggest its organization in centrioles.
Authors: van Breugel, M. / Hirono, M. / Andreeva, A. / Yanagisawa, H.A. / Yamaguchi, S. / Nakazawa, Y. / Morgner, N. / Petrovich, M. / Ebong, I.O. / Robinson, C.V. / Johnson, C.M. / Veprintsev, D. / Zuber, B.
History
DepositionDec 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 1, 2024Group: 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
B: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
C: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
D: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)73,0954
Polymers73,0954
Non-polymers00
Water7,188399
1
A: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)18,2741
Polymers18,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)18,2741
Polymers18,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)18,2741
Polymers18,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)18,2741
Polymers18,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 95.270, 129.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9776, -0.2104, 0.009823), (0.2101, 0.9774, 0.02489), (-0.01484, -0.02227, 0.9996)-35.87, -28.81, 5.335
2given(0.839, -0.5411, 0.05827), (0.544, 0.8306, -0.1194), (0.0162, 0.1319, 0.9911)7.517, -49.96, -2.008
3given(0.9705, 0.2346, -0.05621), (0.2406, -0.9577, 0.1578), (-0.01681, -0.1667, -0.9859)-2.415, -26.84, -3.514

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Components

#1: Protein
SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG / SAS6


Mass: 18273.865 Da / Num. of mol.: 4 / Fragment: HEAD DOMAIN, RESIDUES 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: CDNA FROM ZEBRAFISH / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q7ZVT3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL THREE RESIDUES (GPH) STEM FROM THE EXPRESSION VECTOR. THE S102N MUTATION PROBABLY ...THE N-TERMINAL THREE RESIDUES (GPH) STEM FROM THE EXPRESSION VECTOR. THE S102N MUTATION PROBABLY STEMS FROM STRAIN VARIATION. IT WAS FOUND IN ALL INDEPENDENT PCR REACTIONS MADE WITH THE CDNA. S102 IS NON-CONSERVED EVOLUTIONARILY AND STRUCTURALLY IS SITUATED IN A LOOP REGION.

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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: 2.9 Å3/Da / Density % sol: 57.66 %
Description: THE SELENOMETHIONINE DERIVATIVE STRUCTURE WAS SOLVED BY MAD USING A DERIVATIVE OF A L57M,L90M MUTANT. AN INITIAL MODEL WAS BUILT USING THE EXPERIMENTAL ELECTRON DENSITY MAP AND THEN USED ...Description: THE SELENOMETHIONINE DERIVATIVE STRUCTURE WAS SOLVED BY MAD USING A DERIVATIVE OF A L57M,L90M MUTANT. AN INITIAL MODEL WAS BUILT USING THE EXPERIMENTAL ELECTRON DENSITY MAP AND THEN USED FOR MOLECULAR REPLACEMENT AGAINST THE NATIVE DATASET.
Crystal growpH: 8.5 / Details: 0.1 M TRIS PH 8.5, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→54.8 Å / Num. obs: 63745 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.4
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SE-MET DERIVATIVE

Resolution: 1.92→54.799 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 26.81 / Stereochemistry target values: ML
Details: RESIDUES A-2, C-2, AND C145 TO C156, D-2 TO D0, AND D155-D156, ARE DISORDERED. LOOP REGION C112 TO C120 SHOWED POOR ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2465 3238 5.1 %
Rwork0.2259 --
obs0.227 63668 99.22 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.852 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.0119 Å20 Å20 Å2
2--15.8091 Å20 Å2
3----6.9277 Å2
Refinement stepCycle: LAST / Resolution: 1.92→54.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 0 399 5404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025125
X-RAY DIFFRACTIONf_angle_d0.6636938
X-RAY DIFFRACTIONf_dihedral_angle_d11.5961966
X-RAY DIFFRACTIONf_chiral_restr0.045822
X-RAY DIFFRACTIONf_plane_restr0.002886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.916-1.94460.40871400.34652500X-RAY DIFFRACTION97
1.9446-1.9750.34931390.32812595X-RAY DIFFRACTION99
1.975-2.00740.32631300.3022585X-RAY DIFFRACTION99
2.0074-2.0420.29791320.27892595X-RAY DIFFRACTION99
2.042-2.07920.33551430.27752587X-RAY DIFFRACTION99
2.0792-2.11920.30291480.2712572X-RAY DIFFRACTION99
2.1192-2.16240.30271180.24972644X-RAY DIFFRACTION99
2.1624-2.20940.32121300.24152554X-RAY DIFFRACTION99
2.2094-2.26080.26171430.23722617X-RAY DIFFRACTION99
2.2608-2.31740.2521540.23542620X-RAY DIFFRACTION99
2.3174-2.380.2551260.23172630X-RAY DIFFRACTION100
2.38-2.45010.26241380.24692591X-RAY DIFFRACTION99
2.4501-2.52910.28041230.24772653X-RAY DIFFRACTION99
2.5291-2.61950.29481470.24752596X-RAY DIFFRACTION100
2.6195-2.72440.26511540.24762624X-RAY DIFFRACTION100
2.7244-2.84840.24791480.2352633X-RAY DIFFRACTION100
2.8484-2.99860.27661560.22742636X-RAY DIFFRACTION100
2.9986-3.18640.24821540.22192641X-RAY DIFFRACTION100
3.1864-3.43240.23561310.21662668X-RAY DIFFRACTION100
3.4324-3.77770.23691450.20932672X-RAY DIFFRACTION100
3.7777-4.32420.19471220.19112723X-RAY DIFFRACTION100
4.3242-5.44730.19571510.18712717X-RAY DIFFRACTION100
5.4473-54.82130.22921660.23132777X-RAY DIFFRACTION98

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