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- PDB-7kpi: Crystal structure of the SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 7kpi
TitleCrystal structure of the SPOP MATH domain
ComponentsSpeckle-type POZ protein
KeywordsGENE REGULATION / ubiquitin / ligase / adaptor / protein
Function / homology
Function and homology information


protein catabolic process
Similarity search - Function
MATH domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle type BTB/POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUsher, E.T. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK121509 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK124047 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Intrinsically disordered substrates dictate SPOP subnuclear localization and ubiquitination activity.
Authors: Usher, E.T. / Sabri, N. / Rohac, R. / Boal, A.K. / Mittag, T. / Showalter, S.A.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)16,3531
Polymers16,3531
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Purification by gel filtration ensures a homogeneous monomeric population of molecules.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.642, 53.246, 41.596
Angle α, β, γ (deg.)90.000, 101.386, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Speckle-type POZ protein


Mass: 16352.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: D6RDG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5, 23% (w/v) PME 550, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 14537 / % possible obs: 98.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 12.15 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Net I/σ(I): 46
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 9 / Num. unique obs: 693 / CC1/2: 0.982 / Rpim(I) all: 0.12 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVB

3ivb


Resolution: 1.7→40.78 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / Phase error: 21.0904
RfactorNum. reflection% reflection
Rfree0.1957 730 5.02 %
Rwork0.1592 --
obs0.1611 14535 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 146 1282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121222
X-RAY DIFFRACTIONf_angle_d1.23261648
X-RAY DIFFRACTIONf_chiral_restr0.0786171
X-RAY DIFFRACTIONf_plane_restr0.0075210
X-RAY DIFFRACTIONf_dihedral_angle_d10.33561016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.24631440.16872674X-RAY DIFFRACTION96.31
1.83-2.020.20491420.16592734X-RAY DIFFRACTION97.76
2.02-2.310.18591490.15532766X-RAY DIFFRACTION98.21
2.31-2.910.18211450.17782784X-RAY DIFFRACTION99.02
2.91-40.780.19261500.14692847X-RAY DIFFRACTION99.24

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