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- PDB-8x34: ProteinMY -

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Basic information

Entry
Database: PDB / ID: 8x34
TitleProteinMY
ComponentsKelch-like ECH-associated protein 1
KeywordsGENE REGULATION / Kelch / KEAP1 / NRF2
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYilmaz, M. / Gul, M. / Tavli, S. / Okuducu, C. / Gul, B. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: Human KEAP1 Kelch domain at ambient temperature
Authors: Yilmaz, M. / Gul, M. / Tavli, S. / Okuducu, C. / Gul, B. / DeMirci, H.
History
DepositionNov 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: 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
B: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)62,7142
Polymers62,7142
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.644, 75.825, 218.656
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 Kelch-like ECH-associated protein 1


Mass: 31357.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 5 Å3/Da / Density % sol: 75.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 4.0 M Ammonium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→31.15 Å / Num. obs: 24347 / % possible obs: 99.4 % / Redundancy: 49.3 % / Rmerge(I) obs: 0.904 / Net I/σ(I): 2.07
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.992 / Num. unique obs: 3125 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→31.15 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3285 2015 8.28 %
Rwork0.2891 --
obs0.2923 24347 76.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 0 84 4446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.691
X-RAY DIFFRACTIONf_dihedral_angle_d5.221650
X-RAY DIFFRACTIONf_chiral_restr0.047664
X-RAY DIFFRACTIONf_plane_restr0.005806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.4299230.361223X-RAY DIFFRACTION
2.91-2.950.4105190.3884227X-RAY DIFFRACTION22
2.95-3.030.4521730.3947870X-RAY DIFFRACTION42
3.03-3.130.4285750.3832788X-RAY DIFFRACTION39
3.13-3.240.39141510.37491588X-RAY DIFFRACTION77
3.24-3.370.37011681878X-RAY DIFFRACTION91
3.37-3.530.37391740.36121978X-RAY DIFFRACTION96
3.53-3.710.35441792049X-RAY DIFFRACTION100
3.71-3.940.37651910.342087X-RAY DIFFRACTION100
3.94-4.250.35181850.28412076X-RAY DIFFRACTION100
4.25-4.670.2831870.22812101X-RAY DIFFRACTION100
4.68-5.350.26621930.2222098X-RAY DIFFRACTION100
5.35-6.730.3261960.29292138X-RAY DIFFRACTION100
6.73-100.3262010.27822231X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.5841 Å / Origin y: 4.1253 Å / Origin z: 27.62 Å
111213212223313233
T0.3631 Å20.0333 Å20.1026 Å2-0.3781 Å2-0.0081 Å2--0.3691 Å2
L0.5421 °20.2006 °2-0.2738 °2-0.913 °2-0.7452 °2--1.3915 °2
S0.0995 Å °0.1895 Å °0.058 Å °0.0968 Å °0.0499 Å °0.1702 Å °0.1533 Å °0.0478 Å °-0.1763 Å °
Refinement TLS groupSelection details: all

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