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- PDB-5al6: Central Coiled-Coil Domain (CCCD) of Drosophila melanogaster Ana2... -

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Basic information

Entry
Database: PDB / ID: 5al6
TitleCentral Coiled-Coil Domain (CCCD) of Drosophila melanogaster Ana2. A natural, parallel, tetrameric coiled-coil bundle.
ComponentsANASTRAL SPINDLE 2
KeywordsSTRUCTURAL PROTEIN / ANA2 / COILED-COIL / HELICAL-BUNDLE / CENTRIOLE
Function / homology
Function and homology information


ciliary basal body organization / centriole-centriole cohesion / centriole assembly / microtubule anchoring at centrosome / asymmetric neuroblast division / establishment of mitotic spindle orientation / centriole replication / centriole / ciliary basal body / centrosome
Similarity search - Function
Anastral spindle 2, isoform A
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.8 Å
AuthorsCottee, M.A. / 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: ANASTRAL SPINDLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6652
Polymers5,6421
Non-polymers231
Water97354
1
A: ANASTRAL SPINDLE 2
hetero molecules

A: ANASTRAL SPINDLE 2
hetero molecules

A: ANASTRAL SPINDLE 2
hetero molecules

A: ANASTRAL SPINDLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6618
Polymers22,5694
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area7960 Å2
ΔGint-91.1 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.270, 33.270, 74.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2000-

NA

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Components

#1: Protein/peptide ANASTRAL SPINDLE 2 / ANA2


Mass: 5642.298 Da / Num. of mol.: 1 / Fragment: CENTRAL COILED-COIL DOMAIN, RESIDUES 193-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PLIP (CUSTOM) / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): B834 (DE3) / References: UniProt: Q9XZ31
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSODIUM (NA): 1+ CHARGE

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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: 1.89 Å3/Da / Density % sol: 34.82 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM HEPES MIX (71% PH 7.2, 29% PH 8.2), 42% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7293
DetectorType: PILATUS / Detector: PIXEL / Date: May 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.8→30.36 Å / Num. obs: 41451 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.5
Reflection shellResolution: 0.8→0.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UO4, CHAIN A, RESIS 2 TO 31

1uo4


Resolution: 0.8→30.36 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.215 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.01 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS MODELLED IN RIDING POSITIONS AND U REFINED ISOTROPICALLY, NON-H ATOM U REFINED ANISOTROPICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.11564 2099 5.1 %RANDOM
Rwork0.10637 ---
obs0.10681 39348 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 0.8→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms364 0 1 54 419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.019453
X-RAY DIFFRACTIONr_bond_other_d0.0020.02433
X-RAY DIFFRACTIONr_angle_refined_deg2.231.955616
X-RAY DIFFRACTIONr_angle_other_deg1.0533.002995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.542558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.84626.45231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1811594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.216153
X-RAY DIFFRACTIONr_chiral_restr0.10.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02553
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02114
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1540.795208
X-RAY DIFFRACTIONr_mcbond_other2.0462.102206
X-RAY DIFFRACTIONr_mcangle_it1.7561.157261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0431.08245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.3373453
X-RAY DIFFRACTIONr_sphericity_free25.70958
X-RAY DIFFRACTIONr_sphericity_bonded12.4835491
LS refinement shellResolution: 0.8→0.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 119 -
Rwork0.211 2338 -
obs--79.05 %

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