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- PDB-5a6r: Crystal structure of the BTB domain of human KCTD17 -

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Basic information

Entry
Database: PDB / ID: 5a6r
TitleCrystal structure of the BTB domain of human KCTD17
ComponentsBTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17
KeywordsHYDROLASE
Function / homology
Function and homology information


positive regulation of cilium assembly / cell projection organization / endoplasmic reticulum calcium ion homeostasis / Cul3-RING ubiquitin ligase complex / cullin family protein binding / protein homooligomerization / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum / identical protein binding / cytoplasm
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 KCTD17
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPinkas, D.M. / Sorrell, F. / Sanvitale, C.E. / Goubin, S. / Williams, E. / Newman, J.A. / Pearce, N.M. / Neshich, I. / Pike, A.C.W. / MacKenzie, A. ...Pinkas, D.M. / Sorrell, F. / Sanvitale, C.E. / Goubin, S. / Williams, E. / Newman, J.A. / Pearce, N.M. / Neshich, I. / Pike, A.C.W. / MacKenzie, A. / Quigley, A. / Faust, B. / Carpenter, E.P. / Tallant, C. / Kopec, J. / Chalk, R. / 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
DepositionJun 30, 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 KCTD17
B: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17
C: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17
D: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17
E: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)76,8525
Polymers76,8525
Non-polymers00
Water1448
1
A: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)15,3701
Polymers15,3701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)15,3701
Polymers15,3701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)15,3701
Polymers15,3701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)15,3701
Polymers15,3701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17


Theoretical massNumber of molelcules
Total (without water)15,3701
Polymers15,3701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)285.743, 285.743, 285.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein
BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD17 / KCTD17


Mass: 15370.342 Da / Num. of mol.: 5 / Fragment: BTB DOMAIN, RESIDUES 20-131
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: Q8N5Z5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.13 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 8.5 / Details: 18% MPD -- 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.85→86.15 Å / Num. obs: 23906 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 13.8 % / Biso Wilson estimate: 97.31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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 3DRZ

3drz


Resolution: 2.85→86.155 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1211 5.1 %
Rwork0.2202 --
obs0.2213 23899 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.63 Å2
Refinement stepCycle: LAST / Resolution: 2.85→86.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 0 8 4062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034119
X-RAY DIFFRACTIONf_angle_d0.5525546
X-RAY DIFFRACTIONf_dihedral_angle_d11.3471563
X-RAY DIFFRACTIONf_chiral_restr0.024611
X-RAY DIFFRACTIONf_plane_restr0.003726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.96410.3531290.33612464X-RAY DIFFRACTION100
2.9641-3.09910.33811390.30762453X-RAY DIFFRACTION100
3.0991-3.26240.28991350.27482474X-RAY DIFFRACTION100
3.2624-3.46690.27611420.26662472X-RAY DIFFRACTION100
3.4669-3.73450.24921140.23372507X-RAY DIFFRACTION100
3.7345-4.11040.25651270.212511X-RAY DIFFRACTION100
4.1104-4.70510.2061350.18452521X-RAY DIFFRACTION100
4.7051-5.92770.24311590.19942549X-RAY DIFFRACTION100
5.9277-86.19410.21611310.21812737X-RAY DIFFRACTION99

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