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- PDB-5bxd: Crystal structure of pentameric KCTD1 BTB domain form 2 -

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Basic information

Entry
Database: PDB / ID: 5bxd
TitleCrystal structure of pentameric KCTD1 BTB domain form 2
ComponentsBTB/POZ domain-containing protein KCTD1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


Negative regulation of activity of TFAP2 (AP-2) family transcription factors / transcription factor binding / protein homooligomerization / transcription corepressor activity / negative regulation of DNA-templated transcription / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / BTB/POZ domain-containing protein KCTD1/15, C-terminal domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily ...: / : / BTB/POZ domain-containing protein KCTD1/15, C-terminal domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 KCTD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 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 KCTD1
B: BTB/POZ domain-containing protein KCTD1
C: BTB/POZ domain-containing protein KCTD1
D: BTB/POZ domain-containing protein KCTD1
E: BTB/POZ domain-containing protein KCTD1


Theoretical massNumber of molelcules
Total (without water)63,5575
Polymers63,5575
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-3 kcal/mol
Surface area25360 Å2
Unit cell
Length a, b, c (Å)46.064, 90.839, 127.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
BTB/POZ domain-containing protein KCTD1 / Potassium channel tetramerization domain-containing protein 1


Mass: 12711.461 Da / Num. of mol.: 5 / Fragment: residues 29-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD1, C18orf5 / Plasmid: pMCSG7 / Details (production host): 6xHis-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Codon+ / References: UniProt: Q719H9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: Thin rods, not twinned
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25 mg/mL KCTD1 BTB domain with: 0.1 M MES pH 5, 10% w/v PEG 6000. 1:1 ratio
PH range: 4.8-5.2

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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: Jan 11, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.796→41.08 Å / Num. obs: 50809 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.02157 / Net I/σ(I): 16.98
Reflection shellResolution: 1.796→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.37 / % possible all: 99.52

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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: 1.796→41.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2480 4.88 %
Rwork0.2025 --
obs0.2036 50809 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.9 Å2
Refinement stepCycle: LAST / Resolution: 1.796→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 328 4698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034480
X-RAY DIFFRACTIONf_angle_d0.8296051
X-RAY DIFFRACTIONf_dihedral_angle_d12.5031695
X-RAY DIFFRACTIONf_chiral_restr0.03642
X-RAY DIFFRACTIONf_plane_restr0.004774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7959-1.83050.34981210.31142676X-RAY DIFFRACTION100
1.8305-1.86780.3381320.29682620X-RAY DIFFRACTION99
1.8678-1.90850.29321400.27252647X-RAY DIFFRACTION100
1.9085-1.95290.31371450.26972625X-RAY DIFFRACTION100
1.9529-2.00170.30711330.26052679X-RAY DIFFRACTION100
2.0017-2.05580.29391370.24252619X-RAY DIFFRACTION100
2.0558-2.11630.27441350.23082670X-RAY DIFFRACTION100
2.1163-2.18460.22391430.21962657X-RAY DIFFRACTION100
2.1846-2.26270.22031400.21212648X-RAY DIFFRACTION100
2.2627-2.35330.19771270.21612669X-RAY DIFFRACTION100
2.3533-2.46040.26291450.21032674X-RAY DIFFRACTION100
2.4604-2.590.23071580.20412663X-RAY DIFFRACTION100
2.59-2.75230.27231330.21612707X-RAY DIFFRACTION100
2.7523-2.96470.29451350.21352677X-RAY DIFFRACTION100
2.9647-3.2630.2241340.19492720X-RAY DIFFRACTION100
3.263-3.73490.18991460.17492708X-RAY DIFFRACTION100
3.7349-4.70450.17661430.16512758X-RAY DIFFRACTION100
4.7045-41.09440.19541330.19162912X-RAY DIFFRACTION100
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)
13.3880.9116-0.03152.9561-0.73421.3379-0.40780.59620.0376-0.95620.2374-0.0464-0.03660.21460.18121.1239-0.07530.1730.82460.02350.600915.047985.5144121.328
22.7228-0.25241.00783.48340.23145.7971-0.14990.4062-0.3505-0.42470.0486-0.60970.59360.33080.07840.7448-0.02970.24810.4334-0.12480.72629.449375.2863139.9831
33.89390.01050.48535.0878-0.4414.8855-0.0591-0.0291-0.46390.1685-0.0348-0.34520.10280.08060.09930.2461-0.01720.02250.13320.0190.31012.601488.3776156.4097
43.77451.29240.11243.63720.11772.76810.0779-0.1229-0.13980.3636-0.0115-0.1088-0.0520.0588-0.05260.19590.017-0.00880.141-0.01890.12273.9333110.373154.2832
53.83470.40431.27532.26390.6162.7695-0.07320.06320.1620.10160.0284-0.1166-0.22170.19290.0660.1643-0.00820.00340.18770.01610.129413.5717120.0317137.3064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 29:129)
2X-RAY DIFFRACTION2(chain B and resseq 27:130)
3X-RAY DIFFRACTION3(chain C and resseq 27:130)
4X-RAY DIFFRACTION4(chain D and resseq 26:132)
5X-RAY DIFFRACTION5(chain E and resseq 27:132)

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