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- PDB-4hs2: Crystal Structure of the Human SPOP C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4hs2
TitleCrystal Structure of the Human SPOP C-terminal Domain
ComponentsSpeckle-type POZ protein
KeywordsPROTEIN BINDING / protein interaction domain / Oligomerisation
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsVan Geersdaele, L.K. / Stead, M.A. / Carr, S.B. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP.
Authors: van 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
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)11,9411
Polymers11,9411
Non-polymers00
Water1,11762
1
A: Speckle-type POZ protein

A: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)23,8832
Polymers23,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area1370 Å2
ΔGint-13 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.650, 57.650, 102.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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Components

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


Mass: 11941.446 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 270-374) / Mutation: L273D, L282D, L285K
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; B834 / References: UniProt: O43791
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 1500, 7% isopropanol, 0.1M CaCl2, 0.1M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I04-110.9173
SYNCHROTRONDiamond I0220.9795
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2011
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91731
20.97951
ReflectionRedundancy: 71.5 % / Av σ(I) over netI: 3.4 / Number: 442290 / Rsym value: 0.185 / D res high: 2.125 Å / D res low: 51.405 Å / Num. obs: 6183 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.551.499.810.0310.03153.4
6.729.510010.0420.04258.6
5.496.7210010.0820.08265.8
4.755.4910010.0760.07670.9
4.254.7510010.0680.06874.9
3.884.2510010.0810.08164.8
3.593.8810010.1010.10169.4
3.363.5999.610.1220.12272.8
3.173.3610010.1720.17274.7
33.1710010.1920.19275.6
2.86310010.2490.24977.8
2.742.8610010.2620.26272.7
2.642.7410010.3270.32768.7
2.542.6410010.3630.36373.5
2.452.5410010.4420.44276
2.382.4599.710.4570.45776.2
2.32.3810010.5570.55775.7
2.242.310010.6440.64474.7
2.182.2410010.8850.88571.9
2.122.1810010.8990.89960.1
ReflectionResolution: 1.528→51.405 Å / Num. all: 16004 / Num. obs: 16004 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rsym value: 0.056 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.53-1.578.30.6471.2954011430.64799.9
1.57-1.6110.80.5251.51230011400.52599.9
1.61-1.6612.30.4111.91334910810.41199.9
1.66-1.7112.30.3352.31312910670.33599.9
1.71-1.7612.30.253.11246010170.2599.8
1.76-1.8312.30.2013.9122299980.20199.8
1.83-1.912.40.1684.7120269730.168100
1.9-1.9712.20.1196.4114629410.11999.9
1.97-2.0612.20.0898.7111439150.089100
2.06-2.1612.30.06811104188460.068100
2.16-2.2812.20.05812.6101888360.058100
2.28-2.4212.20.04914.795997880.049100
2.42-2.5812.10.04714.388267270.04799.6
2.58-2.7911.90.04114.683157010.041100
2.79-3.0611.30.03916.373476530.039100
3.06-3.4211.20.03716.566205920.037100
3.42-3.9411.40.03616.460375310.03699.8
3.94-4.83110.03118.751274650.031100
4.83-6.8310.90.0321940203690.032100
6.83-51.4058.60.02822.318942210.02891.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.53→27.75 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1444 / WRfactor Rwork: 0.1267 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9316 / SU B: 1.61 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0512 / SU Rfree: 0.0469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1512 794 5 %RANDOM
Rwork0.132 ---
obs0.1329 15153 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.41 Å2 / Biso mean: 21.2669 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 0 62 551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019558
X-RAY DIFFRACTIONr_bond_other_d0.0010.02337
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.932771
X-RAY DIFFRACTIONr_angle_other_deg0.9573842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.196577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9252625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9671590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.714151
X-RAY DIFFRACTIONr_chiral_restr0.0720.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02107
X-RAY DIFFRACTIONr_rigid_bond_restr6.3733894
X-RAY DIFFRACTIONr_sphericity_free30.104525
X-RAY DIFFRACTIONr_sphericity_bonded14.2815916
LS refinement shellResolution: 1.528→1.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 52 -
Rwork0.218 944 -
all-996 -
obs--99.9 %

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