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- PDB-7exi: Crystal structure of the BTB domain human Keap1 -

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Basic information

Entry
Database: PDB / ID: 7exi
TitleCrystal structure of the BTB domain human Keap1
ComponentsKelch-like ECH-associated protein 1
KeywordsSIGNALING PROTEIN / BTB domain / Keap1 / Nrf2 regulator
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 / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / 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
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPadmanabhan, B. / Deshmukh, P. / Gopinath, K. / Unni, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2015/000735 India
CitationJournal: To Be Published
Title: Crystal structure of the BTB domain human Keap1
Authors: Padmanabhan, B. / Deshmukh, P. / Gopinath, K. / Unni, S.
History
DepositionMay 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,6471
Polymers15,6471
Non-polymers00
Water1,18966
1
A: Kelch-like ECH-associated protein 1

A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)31,2942
Polymers31,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3900 Å2
ΔGint-37 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.976, 42.976, 266.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 15647.005 Da / Num. of mol.: 1 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Li Acetate, TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 13888 / % possible obs: 97.8 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.023 / Rrim(I) all: 0.093 / Χ2: 0.981 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.8614.61.4416960.7720.3861.4930.374100
1.86-1.9142.0786620.7530.5722.1580.4100
1.9-1.9312.60.6556740.7870.1810.6810.55799.6
1.93-1.9716.31.0326940.9410.2631.0660.449100
1.97-2.0117.10.6926740.9320.1720.7140.453100
2.01-2.06170.5176840.9570.1280.5330.495100
2.06-2.1116.90.4026720.9730.10.4140.604100
2.11-2.1717.30.3157020.9770.0770.3240.638100
2.17-2.2312.70.3266610.9690.0910.3390.63397.3
2.23-2.3110.70.2666430.9630.0760.2780.99493.5
2.31-2.3917.50.2067140.9940.0510.2120.831100
2.39-2.4817.70.1786850.9910.0430.1840.91699.6
2.48-2.617.90.1536930.9940.0370.1581.13699.6
2.6-2.7317.20.1367060.9980.0330.141.23899.9
2.73-2.917.20.1137100.9980.0280.1161.46100
2.9-3.1315.80.0987220.9980.0250.1011.51699.6
3.13-3.4413.80.0777160.9980.0210.081.59499.4
3.44-3.9412.10.0726090.9980.020.0751.94281
3.94-4.97160.0647430.9980.0160.0661.78497.3
4.97-5014.90.0598280.9990.0150.0611.57192.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CXI

4cxi


Resolution: 1.82→26.62 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 689 5 %
Rwork0.2089 13100 -
obs0.2108 13789 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.3 Å2 / Biso mean: 54.6864 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 1.82→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 0 66 1064
Biso mean---53.2 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.82-1.970.42721340.3254255499
1.97-2.160.27881370.2222585100
2.16-2.480.27941340.2239256298
2.48-3.120.30931420.23362689100
3.12-100.20031420.1867271093
Refinement TLS params.Method: refined / Origin x: -7.1035 Å / Origin y: 9.8098 Å / Origin z: -15.0143 Å
111213212223313233
T0.5833 Å20.121 Å2-0.0277 Å2-0.2666 Å20.0003 Å2--0.3475 Å2
L2.8459 °2-0.8719 °2-0.1358 °2-2.7921 °2-0.9967 °2--3.1543 °2
S-0.1344 Å °-0.1403 Å °-0.0173 Å °0.2757 Å °0.0325 Å °-0.1017 Å °0.364 Å °0.0324 Å °0.0016 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 50 through 179)

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