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- PDB-9fh8: Crystal structure of the SPD-2 domain of Apis dorsata CEP192 -

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Basic information

Entry
Database: PDB / ID: 9fh8
TitleCrystal structure of the SPD-2 domain of Apis dorsata CEP192
ComponentsCentrosomal protein 192 (CEP192)
KeywordsCELL CYCLE / Centrosome / PCM
Biological speciesApis dorsata (giant honeybee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
Authorsvan Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/3 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
DepositionMay 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein 192 (CEP192)
B: Centrosomal protein 192 (CEP192)
C: Centrosomal protein 192 (CEP192)
D: Centrosomal protein 192 (CEP192)
E: Centrosomal protein 192 (CEP192)
F: Centrosomal protein 192 (CEP192)
G: Centrosomal protein 192 (CEP192)
H: Centrosomal protein 192 (CEP192)


Theoretical massNumber of molelcules
Total (without water)309,4968
Polymers309,4968
Non-polymers00
Water00
1
A: Centrosomal protein 192 (CEP192)
G: Centrosomal protein 192 (CEP192)

B: Centrosomal protein 192 (CEP192)
F: Centrosomal protein 192 (CEP192)


Theoretical massNumber of molelcules
Total (without water)154,7484
Polymers154,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-y+1/2,x,z-1/41
Buried area6490 Å2
ΔGint-57 kcal/mol
Surface area53400 Å2
MethodPISA
2
C: Centrosomal protein 192 (CEP192)
H: Centrosomal protein 192 (CEP192)

D: Centrosomal protein 192 (CEP192)
E: Centrosomal protein 192 (CEP192)


Theoretical massNumber of molelcules
Total (without water)154,7484
Polymers154,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x,z-1/41
Buried area6410 Å2
ΔGint-49 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.300, 183.300, 190.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
Centrosomal protein 192 (CEP192)


Mass: 38687.008 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis dorsata (giant honeybee) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: phospholipase A2
Has ligand of interestY
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 17% PEG3350, 0.25 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 3.5→49.48 Å / Num. obs: 39530 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.072 / Rrim(I) all: 0.125 / Net I/σ(I): 10.4
Reflection shellResolution: 3.5→3.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4459 / CC1/2: 0.599 / Rpim(I) all: 0.669 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→43.29 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3131 2024 5.13 %
Rwork0.2875 --
obs0.2889 39490 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16742 0 0 0 16742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317054
X-RAY DIFFRACTIONf_angle_d0.74623000
X-RAY DIFFRACTIONf_dihedral_angle_d6.2612203
X-RAY DIFFRACTIONf_chiral_restr0.052642
X-RAY DIFFRACTIONf_plane_restr0.0042878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.4041140.37522701X-RAY DIFFRACTION100
3.59-3.680.34151560.35722631X-RAY DIFFRACTION100
3.68-3.790.38451640.35212650X-RAY DIFFRACTION100
3.79-3.920.36161550.34662688X-RAY DIFFRACTION100
3.92-4.060.37131310.3282668X-RAY DIFFRACTION100
4.06-4.220.3169900.31842719X-RAY DIFFRACTION100
4.22-4.410.32441190.31042695X-RAY DIFFRACTION100
4.41-4.640.30481610.27712657X-RAY DIFFRACTION100
4.64-4.930.25451170.25742700X-RAY DIFFRACTION100
4.93-5.310.29841800.262634X-RAY DIFFRACTION100
5.31-5.840.33411550.27382665X-RAY DIFFRACTION100
5.85-6.690.31291770.31282666X-RAY DIFFRACTION100
6.69-8.420.30841420.29012693X-RAY DIFFRACTION100
8.42-43.290.28981630.24142699X-RAY DIFFRACTION99

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