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- PDB-5bxh: Crystal structure of pentameric KCTD9 BTB domain -

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Basic information

Entry
Database: PDB / ID: 5bxh
TitleCrystal structure of pentameric KCTD9 BTB domain
ComponentsBTB/POZ domain-containing protein KCTD9
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


cullin family protein binding / protein homooligomerization / intracellular signal transduction / protein ubiquitination / identical protein binding
Similarity search - Function
: / Pentapeptide repeats (8 copies) / Doublecortin domain superfamily / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Pentapeptide repeat / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A ...: / Pentapeptide repeats (8 copies) / Doublecortin domain superfamily / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Pentapeptide repeat / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BTB/POZ domain-containing protein KCTD9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsJi, A.X. / Chu, A. / Prive, G.G.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Insights into KCTD Protein Assembly and Cullin3 Recognition.
Authors: Ji, A.X. / Chu, A. / Nielsen, T.K. / Benlekbir, S. / Rubinstein, J.L. / Prive, G.G.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection / Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB/POZ domain-containing protein KCTD9
B: BTB/POZ domain-containing protein KCTD9
C: BTB/POZ domain-containing protein KCTD9
D: BTB/POZ domain-containing protein KCTD9
E: BTB/POZ domain-containing protein KCTD9


Theoretical massNumber of molelcules
Total (without water)60,4585
Polymers60,4585
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-13 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.396, 105.396, 97.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
BTB/POZ domain-containing protein KCTD9


Mass: 12091.656 Da / Num. of mol.: 5 / Fragment: BTB domain residues 89-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD9 / Plasmid: pMCSG7 / Details (production host): 6xHis-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Codon+ / References: UniProt: Q7L273

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 mg/mL KCTD9 BTB domain with: 0.17 M Lithium citrate, 16% w/v PEG 3350. 1:1 ratio
Temp details: crystals grown in cold room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→30.57 Å / Num. obs: 16374 / % possible obs: 99.67 % / Redundancy: 9.8 % / Biso Wilson estimate: 94.16 Å2 / Rmerge(I) obs: 0.05735 / Net I/σ(I): 10.09
Reflection shellResolution: 2.76→2.858 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.46 / % possible all: 99.63

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692phasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRZ

3drz


Resolution: 2.76→30.566 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 817 4.99 %
Rwork0.2345 --
obs0.2367 16373 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.2 Å2
Refinement stepCycle: LAST / Resolution: 2.76→30.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 0 0 4014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034096
X-RAY DIFFRACTIONf_angle_d0.7365530
X-RAY DIFFRACTIONf_dihedral_angle_d14.1651496
X-RAY DIFFRACTIONf_chiral_restr0.025609
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.93280.48511340.41962546X-RAY DIFFRACTION100
2.9328-3.15910.41371300.37142552X-RAY DIFFRACTION100
3.1591-3.47660.32851360.28942570X-RAY DIFFRACTION100
3.4766-3.97870.3331320.25312583X-RAY DIFFRACTION100
3.9787-5.00920.27021400.21792605X-RAY DIFFRACTION100
5.0092-30.56760.22821450.19522700X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6118-2.139-0.85517.71970.87714.86840.08490.9043-0.8456-0.3928-0.21781.39940.3101-0.96990.16760.7715-0.2469-0.07811.3029-0.25051.08482.295482.0022109.6888
26.8347-0.4390.59426.770.32496.24560.1260.86731.0457-0.5410.09410.8638-0.5832-0.5366-0.10860.7135-0.0227-0.09031.06870.14641.15384.1535104.0095109.6946
36.29890.5315-1.41475.771-1.31365.65420.17321.1486-1.542-0.5298-0.1162-0.57590.57830.299-0.0640.726-0.03040.04271.0535-0.37341.178222.868473.533109.5111
46.7353-0.15041.30175.089-0.49924.98710.03441.17221.7058-0.1637-0.2638-0.5513-0.8570.41730.20020.9112-0.25850.03671.19890.36541.462325.2458109.4312110.2126
53.6590.9162-0.54398.7396-0.02974.2773-0.06161.260.0244-0.2931-0.0011-2.0870.01080.8943-0.01810.6175-0.10090.09461.4831-0.0081.403737.154190.6218109.4523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:106)
2X-RAY DIFFRACTION2(chain B and resseq 2:106)
3X-RAY DIFFRACTION3(chain C and resseq 2:106)
4X-RAY DIFFRACTION4(chain D and resseq 3:106)
5X-RAY DIFFRACTION5(chain E and resseq 4:106)

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