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- PDB-5yq4: Crystal structure of kelch domain of KLHL20 -

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Basic information

Entry
Database: PDB / ID: 5yq4
TitleCrystal structure of kelch domain of KLHL20
ComponentsKelch-like protein 20
KeywordsPROTEIN BINDING / kelch domain / KLHL20
Function / homology
Function and homology information


type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity ...type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein transport / actin cytoskeleton / Neddylation / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / axon / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Kelch-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsYeh, M.C. / Ho, M.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-104-TP-B05 Taiwan
CitationJournal: To Be Published
Title: The crystal structure of kelch domain of KLHL20
Authors: Yeh, M.C. / Ho, M.C.
History
DepositionNov 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like protein 20


Theoretical massNumber of molelcules
Total (without water)32,5531
Polymers32,5531
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)49.957, 74.203, 155.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

21A-899-

HOH

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Components

#1: Protein Kelch-like protein 20 / KLHL20 / Kelch-like ECT2-interacting protein / Kelch-like protein X


Mass: 32552.654 Da / Num. of mol.: 1 / Fragment: kelch domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL20, KLEIP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2M5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Sodium Citrate, pH 5, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 28, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. obs: 40146 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Rrim(I) all: 0.052 / Χ2: 0.915 / Net I/σ(I): 12.4 / Num. measured all: 384030
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.648.60.23639370.9850.0840.2510.85799.5
1.64-1.79.40.20539450.9910.070.2170.866100
1.7-1.789.60.16939810.9930.0570.1780.909100
1.78-1.879.70.12439940.9950.0410.130.954100
1.87-1.999.80.09739820.9960.0330.1031.05100
1.99-2.149.80.07939750.9970.0260.0831.161100
2.14-2.369.80.06140200.9980.020.0640.996100
2.36-2.79.80.04840270.9980.0160.0510.855100
2.7-3.49.80.04140640.9990.0140.0430.944100
3.4-209.40.02842210.9980.0090.0290.55699.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.298 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.078
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 2069 5.2 %RANDOM
Rwork0.1631 ---
obs0.1646 38031 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.09 Å2 / Biso mean: 15.052 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0 Å2
2--0.33 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 230 2390
Biso mean---25.4 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192266
X-RAY DIFFRACTIONr_bond_other_d0.0050.022068
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.9433097
X-RAY DIFFRACTIONr_angle_other_deg1.1534778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0675307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.24222.42499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6615359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.721523
X-RAY DIFFRACTIONr_chiral_restr0.1530.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022617
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02506
LS refinement shellResolution: 1.577→1.618 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 141 -
Rwork0.175 2680 -
all-2821 -
obs--95.95 %

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