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- PDB-6g57: Structure of the H1 domain of human KCTD8 -

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Basic information

Entry
Database: PDB / ID: 6g57
TitleStructure of the H1 domain of human KCTD8
ComponentsBTB/POZ domain-containing protein KCTD8
KeywordsLIGASE / KCTD8 / C-terminal Domain / H1 domain
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / presynaptic membrane / postsynaptic membrane / receptor complex
Similarity search - Function
: / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
BTB/POZ domain-containing protein KCTD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Strain-Damerell, C.M. / Fairhead, M. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Structure of the H1 domain of human KCTD8
Authors: Pinkas, D.M.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 KCTD8
B: BTB/POZ domain-containing protein KCTD8
C: BTB/POZ domain-containing protein KCTD8
D: BTB/POZ domain-containing protein KCTD8


Theoretical massNumber of molelcules
Total (without water)57,7494
Polymers57,7494
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-28 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.117, 92.117, 219.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
BTB/POZ domain-containing protein KCTD8


Mass: 14437.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6ZWB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50% PEG200 -- 0.2M sodium chloride -- 0.1M sodium/potassium phosphate pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.75→79.79 Å / Num. obs: 15121 / % possible obs: 100 % / Redundancy: 18.5 % / Net I/σ(I): 16.1
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 18.1 % / Num. unique obs: 1070 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human KCTD16 H1 (unpublished)

Resolution: 2.8→79.775 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.39
RfactorNum. reflection% reflection
Rfree0.3421 693 5.22 %
Rwork0.2954 --
obs0.2963 13264 92.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→79.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 0 11 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012708
X-RAY DIFFRACTIONf_angle_d0.2993647
X-RAY DIFFRACTIONf_dihedral_angle_d17.1611536
X-RAY DIFFRACTIONf_chiral_restr0.033405
X-RAY DIFFRACTIONf_plane_restr0.001457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.01620.46051160.42322072X-RAY DIFFRACTION79
3.0162-3.31980.35161240.34322358X-RAY DIFFRACTION89
3.3198-3.80010.35841530.30312542X-RAY DIFFRACTION96
3.8001-4.78770.31641300.25952706X-RAY DIFFRACTION99
4.7877-79.80770.33611700.29272893X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.4722 Å / Origin y: 52.63 Å / Origin z: 93.8565 Å
111213212223313233
T0.4625 Å2-0.0127 Å20.0951 Å2-0.4274 Å20.0283 Å2--0.4911 Å2
L0.0715 °20.0793 °20.0594 °2-0.1549 °2-0.0919 °2--0.4099 °2
S0.0242 Å °0.135 Å °-0.0043 Å °0.0518 Å °-0.0343 Å °-0.0262 Å °0.0018 Å °-0.1444 Å °-0 Å °
Refinement TLS groupSelection details: all

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