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- PDB-3drz: X-ray crystal structure of the N-terminal BTB domain of human KCT... -

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Basic information

Entry
Database: PDB / ID: 3drz
TitleX-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein
ComponentsBTB/POZ domain-containing protein KCTD5
KeywordsUNKNOWN FUNCTION / KCTD5 / BTB/POZ / potassium channel domain T1 / PENTAMER
Function / homology
Function and homology information


Cul3-RING ubiquitin ligase complex / cullin family protein binding / protein homooligomerization / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex binding / identical protein binding / nucleus / cytoplasm / cytosol
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 KCTD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTereshko, V. / Dementieva, I. / Goldstein, S.A.N.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Pentameric assembly of potassium channel tetramerization domain-containing protein 5.
Authors: Dementieva, I.S. / Tereshko, V. / McCrossan, Z.A. / Solomaha, E. / Araki, D. / Xu, C. / Grigorieff, N. / Goldstein, S.A.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 KCTD5
B: BTB/POZ domain-containing protein KCTD5
C: BTB/POZ domain-containing protein KCTD5
D: BTB/POZ domain-containing protein KCTD5
E: BTB/POZ domain-containing protein KCTD5


Theoretical massNumber of molelcules
Total (without water)61,6055
Polymers61,6055
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.039, 90.718, 110.158
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 KCTD5


Mass: 12320.969 Da / Num. of mol.: 5 / Fragment: N-terminal domain, UNP residues 40-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: MODIFIED VECTOR, TEV PROTEASE CLEAVAGE SITE REPLACING THROMBIN SITE
Gene: KCTD5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NXV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 24% (w/v) PEG 3350, 100 mM MgCl2, 100 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46924 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.15
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.32 / Num. unique all: 3090 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0073refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DRX

3drx


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.421 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23226 2374 5.1 %RANDOM
Rwork0.19357 ---
all0.19548 44550 --
obs0.19548 44550 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---2.62 Å20 Å2
3---3.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 359 4425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9835644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6725496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71523.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85615771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8251540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.52464
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67723992
X-RAY DIFFRACTIONr_scbond_it2.39631712
X-RAY DIFFRACTIONr_scangle_it3.8144.51647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 202 -
Rwork0.235 3090 -
obs--98.42 %
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)
11.7121-0.86250.47682.566-0.30262.1987-0.0093-0.249-0.17850.2632-0.02640.3710.1995-0.11130.0358-0.0401-0.04560.0192-0.04250.0563-0.0148-14.2065-10.497118.5026
21.6374-0.0956-0.11522.19790.22241.74670.02850.08640.077-0.08550.00340.0974-0.049-0.126-0.0318-0.06990.0164-0.0265-0.05180.0165-0.0512-14.39667.33475.9032
32.19750.0155-0.14352.25250.22791.20970.06650.10410.1074-0.1690.0194-0.0652-0.1090.1124-0.0859-0.0228-0.01870.0153-0.04930.0196-0.07456.45110.98910.3067
42.31940.17660.58011.5414-0.58132.16430.1291-0.1981-0.28650.0726-0.0016-0.14250.19170.0679-0.1275-0.0494-0.01-0.0176-0.04110.0092-0.02918.8062-3.75399.649
53.63670.04460.40152.08120.36822.26130.06160.1898-0.04990.1175-0.1228-0.18120.07580.28490.0612-0.05530.0508-0.02930.01390.1417-0.14235.9812-17.081821.3861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 95
2X-RAY DIFFRACTION1A96 - 145
3X-RAY DIFFRACTION1A1001 - 1074
4X-RAY DIFFRACTION2B43 - 95
5X-RAY DIFFRACTION2B96 - 145
6X-RAY DIFFRACTION2B1000 - 1089
7X-RAY DIFFRACTION3C44 - 95
8X-RAY DIFFRACTION3C96 - 145
9X-RAY DIFFRACTION3C1008 - 1085
10X-RAY DIFFRACTION4D43 - 95
11X-RAY DIFFRACTION4D96 - 145
12X-RAY DIFFRACTION4D1009 - 1078
13X-RAY DIFFRACTION5E43 - 95
14X-RAY DIFFRACTION5E96 - 145
15X-RAY DIFFRACTION5E1001 - 1095

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