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- PDB-4cxj: BTB domain of KEAP1 C151W mutant -

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Basic information

Entry
Database: PDB / ID: 4cxj
TitleBTB domain of KEAP1 C151W mutant
ComponentsKELCH-LIKE ECH-ASSOCIATED PROTEIN 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsCleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. ...Cleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. / Qi, H. / Sweitzer, T. / Ward, P. / Davies, T.G.
CitationJournal: Plos One / Year: 2014
Title: Structure of the Btb Domain of Keap1 and its Interaction with the Triterpenoid Antagonist Cddo.
Authors: Cleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. / Qi, H. / Sweitzer, T. / Ward, P. / Davies, T.G.
History
DepositionApr 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,3771
Polymers15,3771
Non-polymers00
Water81145
1
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1

A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)30,7532
Polymers30,7532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area4000 Å2
ΔGint-33.9 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.874, 42.874, 267.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

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Components

#1: Protein KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 / CYTOSOLIC INHIBITOR OF NRF2 / INRF2 / KELCH-LIKE PROTEIN 19 / KEAP1


Mass: 15376.718 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN, RESIDUES 48-180 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.31 Å3/Da / Density % sol: 46.73 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→44.61 Å / Num. obs: 4153 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 72.33 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→44.61 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.9182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418 / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 225 5.42 %RANDOM
Rwork0.2114 ---
obs0.2147 4153 99.47 %-
Displacement parametersBiso mean: 70.854 Å2
Baniso -1Baniso -2Baniso -3
1--8.0779 Å20 Å20 Å2
2---8.0779 Å20 Å2
3---16.1558 Å2
Refine analyzeLuzzati coordinate error obs: 0.457 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 45 1072
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081052HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.961423HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d371SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes154HARMONIC5
X-RAY DIFFRACTIONt_it1052HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.15
X-RAY DIFFRACTIONt_other_torsion20.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion138SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1202SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3436 64 5.65 %
Rwork0.2379 1069 -
all0.2434 1133 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 7.442 Å / Origin y: -10.0977 Å / Origin z: -15.2194 Å
111213212223313233
T0.0628 Å20.1061 Å20.0237 Å2--0.2683 Å2-0.0113 Å2---0.1703 Å2
L1.8848 °2-0.9913 °20.0202 °2-3.6593 °21.0755 °2--4.8839 °2
S-0.1657 Å °-0.014 Å °0.0435 Å °0.4426 Å °0.0343 Å °0.3018 Å °-0.5427 Å °-0.0178 Å °0.1314 Å °
Refinement TLS groupSelection details: CHAIN A AND RESI 49 179

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