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- PDB-5a15: Crystal structure of the BTB domain of human KCTD16 -

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Basic information

Entry
Database: PDB / ID: 5a15
TitleCrystal structure of the BTB domain of human KCTD16
ComponentsBTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
KeywordsSIGNALING PROTEIN
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 / 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 KCTD16
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsPinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Canning, P. / Dixon Clarke, S.E. / Talon, R. / Wiggers, H.J. / Fitzpatrick, F. / Tallant, C. ...Pinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Canning, P. / Dixon Clarke, S.E. / Talon, R. / Wiggers, H.J. / Fitzpatrick, F. / Tallant, C. / Kopec, J. / Chalk, R. / Doutch, J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases.
Authors: Pinkas, D.M. / Sanvitale, C.E. / Bufton, J.C. / Sorrell, F.J. / Solcan, N. / Chalk, R. / Doutch, J. / Bullock, A.N.
History
DepositionApr 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 6, 2017Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 KCTD16
B: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
C: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
D: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
E: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
F: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
G: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
H: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
I: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
J: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
K: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
L: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
M: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
N: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
O: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)209,44315
Polymers209,44315
Non-polymers00
Water0
1
A: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.790, 69.370, 134.240
Angle α, β, γ (deg.)102.45, 95.72, 90.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16 / KCTD16 / POTASSIUM CHANNEL TETRAMERIZATION DOMAIN-CONTAINING PROTEIN 16


Mass: 13962.897 Da / Num. of mol.: 15 / Fragment: BTB DOMAIN, UNP RESIDUES 16-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q68DU8

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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: 3.1 Å3/Da / Density % sol: 60.3 % / Description: NONE
Crystal growpH: 6 / Details: 21% PEG3350, 0.1M BIS-TRIS PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.76→36.55 Å / Num. obs: 50928 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 81.92 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.7
Reflection shellResolution: 2.76→2.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UES

4ues
PDB Unreleased entry


Resolution: 2.76→34.65 Å / SU ML: 0.39 / σ(F): 1.96 / Phase error: 33.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2456 4.8 %
Rwork0.2165 --
obs0.2185 50911 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.9 Å2
Refinement stepCycle: LAST / Resolution: 2.76→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11810 0 0 0 11810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312155
X-RAY DIFFRACTIONf_angle_d0.7916463
X-RAY DIFFRACTIONf_dihedral_angle_d19.7957262
X-RAY DIFFRACTIONf_chiral_restr0.0341764
X-RAY DIFFRACTIONf_plane_restr0.0042109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7601-2.81320.38951290.34112661X-RAY DIFFRACTION98
2.8132-2.87060.37781440.32642727X-RAY DIFFRACTION99
2.8706-2.9330.35671200.29442712X-RAY DIFFRACTION98
2.933-3.00110.30431610.26822679X-RAY DIFFRACTION98
3.0011-3.07620.3251340.27312686X-RAY DIFFRACTION98
3.0762-3.15930.29671380.2742738X-RAY DIFFRACTION98
3.1593-3.25220.34431400.27342714X-RAY DIFFRACTION98
3.2522-3.35710.3691200.25022757X-RAY DIFFRACTION99
3.3571-3.47690.29441080.24312717X-RAY DIFFRACTION98
3.4769-3.6160.26321510.23492716X-RAY DIFFRACTION99
3.616-3.78040.28441310.24392689X-RAY DIFFRACTION98
3.7804-3.97940.28371280.23632705X-RAY DIFFRACTION98
3.9794-4.22830.28451530.21012683X-RAY DIFFRACTION98
4.2283-4.55420.23971420.19092692X-RAY DIFFRACTION98
4.5542-5.01120.22011540.19642684X-RAY DIFFRACTION98
5.0112-5.73350.23581320.20352654X-RAY DIFFRACTION96
5.7335-7.21290.27221240.21492619X-RAY DIFFRACTION95
7.2129-34.65340.20081470.17172622X-RAY DIFFRACTION96

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