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- PDB-4j8z: Crystal Structure of the Human SPOP BTB Domain -

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Basic information

Entry
Database: PDB / ID: 4j8z
TitleCrystal Structure of the Human SPOP BTB Domain
ComponentsSpeckle-type POZ protein
KeywordsPROTEIN BINDING / BTB domain / BACK domain / Protein ubiquitination
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #50 / Double Stranded RNA Binding Domain / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A ...Double Stranded RNA Binding Domain - #50 / Double Stranded RNA Binding Domain / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Other non-globular / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsStead, M.A. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP
Authors: Geersdaele, L.K. / Stead, M.A. / Harrison, C.M. / Carr, S.B. / Close, H.J. / Rosbrook, G.O. / Connell, S.D. / Wright, S.C.
History
DepositionFeb 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
B: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)46,7252
Polymers46,7252
Non-polymers00
Water45025
1
A: Speckle-type POZ protein

A: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)46,7252
Polymers46,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area18400 Å2
MethodPISA
2
B: Speckle-type POZ protein

B: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)46,7252
Polymers46,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.390, 71.580, 62.220
Angle α, β, γ (deg.)90.000, 117.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 178 - 353 / Label seq-ID: 15 - 190

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 23362.740 Da / Num. of mol.: 2 / Fragment: SPOP BTB domain, UNP residues 178-374 / Mutation: Y353E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O43791
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.36 Å3/Da / Density % sol: 47.89 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9173 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.42→58.02 Å / Num. all: 16513 / Num. obs: 16513 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Rsym value: 0.052 / Net I/σ(I): 17.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å7.99 Å
Translation4 Å7.99 Å

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→58.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2633 / WRfactor Rwork: 0.2177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7936 / SU B: 9.487 / SU ML: 0.211 / SU R Cruickshank DPI: 0.4009 / SU Rfree: 0.2658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.401 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 835 5.1 %RANDOM
Rwork0.2067 ---
obs0.2091 16512 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.78 Å2 / Biso mean: 64.9351 Å2 / Biso min: 25.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.4 Å2
2---3.02 Å2-0 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.42→58.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 25 2787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192809
X-RAY DIFFRACTIONr_bond_other_d0.0040.022659
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9583793
X-RAY DIFFRACTIONr_angle_other_deg0.97736145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77225.496131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79115505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0491512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023178
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02598
X-RAY DIFFRACTIONr_mcbond_it5.3896.1061422
X-RAY DIFFRACTIONr_mcbond_other5.3896.1041421
X-RAY DIFFRACTIONr_mcangle_it7.7069.1461774
Refine LS restraints NCS

Ens-ID: 1 / Number: 9860 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 56 -
Rwork0.281 1149 -
all-1205 -
obs--98.05 %

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