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- PDB-9c72: Structure of the ASH3 domain of Drosophila melanogaster Spd-2 -

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Basic information

Entry
Database: PDB / ID: 9c72
TitleStructure of the ASH3 domain of Drosophila melanogaster Spd-2
ComponentsSpindle defective 2
KeywordsCYTOSOLIC PROTEIN / Centrosome / pericentriolar material / Drosophila
Function / homology
Function and homology information


sperm aster formation / apyrase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / astral microtubule organization / centrosome cycle / pericentriolar material / centriole / centrosome
Similarity search - Function
ADP-ribose pyrophosphatase, mitochondrial / : / : / : / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsJohnson, S. / Feng, Z. / Lea, S.M. / Raff, J.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104575 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly.
Authors: Hu, L. / Wainman, A. / Andreeva, A. / Apizi, M. / Alvarez-Rodrigo, I. / Wong, S.S. / Saurya, S. / Sheppard, D. / Cottee, M. / Johnson, S. / Lea, S.M. / Raff, J.W. / van Breugel, M. / Feng, Z.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindle defective 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6747
Polymers13,2001
Non-polymers4746
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.580, 88.580, 79.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1201-

SO4

21A-1341-

HOH

31A-1369-

HOH

41A-1379-

HOH

51A-1391-

HOH

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Components

#1: Protein Spindle defective 2


Mass: 13200.053 Da / Num. of mol.: 1 / Fragment: ASH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: spd-2, anon-73Ba, BcDNA.LD24702, BcDNA:LD24702, CEP192, Cep192, CG17286-PA, D-SPD2, D-Spd2, Dmel\CG17286, DSPD-2, DSpd-2, Dspd-2, DSpd2, Dspd2, dSpd2, SPD-2, Spd-2, SPD2, Spd2, spd2, CG17286, Dmel_CG17286
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VV79, ADP-ribose diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2M ammonium sulfate, 5% PEG400, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.93→62.64 Å / Num. obs: 12013 / % possible obs: 99.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 29.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 1.93→2.12 Å / Num. unique obs: 2936 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→62.64 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 573 4.77 %
Rwork0.1731 11429 -
obs0.1747 12002 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→62.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms763 0 27 91 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099826
X-RAY DIFFRACTIONf_angle_d1.04581127
X-RAY DIFFRACTIONf_chiral_restr0.0748128
X-RAY DIFFRACTIONf_plane_restr0.0076148
X-RAY DIFFRACTIONf_dihedral_angle_d13.3046314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.120.25951340.21552802X-RAY DIFFRACTION98.79
2.12-2.430.24121430.19822760X-RAY DIFFRACTION97.42
2.43-3.060.21051590.18082866X-RAY DIFFRACTION99.97
3.06-62.640.19031370.15673001X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: 74.9911204061 Å / Origin y: -5.72377966997 Å / Origin z: 11.5272423135 Å
111213212223313233
T0.167439304356 Å2-0.00204931666721 Å20.0283949637346 Å2-0.143228688287 Å2-0.0318714132575 Å2--0.152933233577 Å2
L2.15543928926 °2-0.176360246179 °20.450942996158 °2-5.42524739012 °2-3.07372597102 °2--4.799123747 °2
S0.00961381646186 Å °-0.0243567210716 Å °0.175422831164 Å °0.220008353742 Å °-0.000741392164435 Å °0.0723682226692 Å °-0.403702606394 Å °-0.0135356326756 Å °-0.0295750917677 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1049 through 1146)

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