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- PDB-4crh: Crystal structure of the BTB-T1 domain of human SHKBP1 -

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Basic information

Entry
Database: PDB / ID: 4crh
TitleCrystal structure of the BTB-T1 domain of human SHKBP1
ComponentsSH3KBP1-BINDING PROTEIN 1
KeywordsPROTEIN-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of epidermal growth factor receptor signaling pathway / protein homooligomerization / lysosome / identical protein binding
Similarity search - Function
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 / Trp-Asp (WD) repeats signature. / WD40 repeats ...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 / Trp-Asp (WD) repeats signature. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH3KBP1-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPinkas, D.M. / Solcan, N. / Krojer, T. / Goubin, S. / Williams, E.P. / 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
DepositionFeb 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Atomic model
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.3Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: SH3KBP1-BINDING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)14,3331
Polymers14,3331
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.290, 71.290, 38.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SH3KBP1-BINDING PROTEIN 1 / SHKBP1


Mass: 14333.148 Da / Num. of mol.: 1 / Fragment: BTB-T1, RESIDUES 18-120
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: Q8TBC3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 8.4 / Details: 17% PEG 2000, MME 0.1M TRIS PH 8.4, 0.15M TMAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.72→38.41 Å / Num. obs: 11971 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.7
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DRX

3drx


Resolution: 1.72→35.645 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 572 4.8 %
Rwork0.1637 --
obs0.1651 11951 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→35.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 0 98 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008787
X-RAY DIFFRACTIONf_angle_d1.2111065
X-RAY DIFFRACTIONf_dihedral_angle_d13.719295
X-RAY DIFFRACTIONf_chiral_restr0.045124
X-RAY DIFFRACTIONf_plane_restr0.007135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7203-1.89340.24821300.20682815X-RAY DIFFRACTION100
1.8934-2.16730.2081380.18352837X-RAY DIFFRACTION100
2.1673-2.73040.22671490.17222834X-RAY DIFFRACTION100
2.7304-35.65260.16771550.14932893X-RAY DIFFRACTION100

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