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- PDB-1u6d: Crystal structure of the Kelch domain of human Keap1 -

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Basic information

Entry
Database: PDB / ID: 1u6d
TitleCrystal structure of the Kelch domain of human Keap1
Componentskelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / beta-propeller / kelch repeat motif
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-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 / 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsLi, X. / Zhang, D. / Hannink, M. / Beamer, L.J.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the kelch domain of human keap1
Authors: Li, X. / Zhang, D. / Hannink, M. / Beamer, L.J.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and initial crystallographic analysis of the Kelch domain from human Keap1
Authors: Li, X. / Zhang, D. / Hannink, M. / Beamer, L.J.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
X: kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,6951
Polymers33,6951
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.892, 85.892, 148.753
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
11X-919-

HOH

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Components

#1: Protein kelch-like ECH-associated protein 1


Mass: 33694.527 Da / Num. of mol.: 1 / Fragment: Kelch
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Keap1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4% PEG 4000, 100 mM Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 28169 / Num. obs: 28169 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 33.9
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2749 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→19.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.351 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18237 1316 5.1 %RANDOM
Rwork0.14766 ---
obs0.14941 24523 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.29 Å20 Å2
2---0.57 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 0 313 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212265
X-RAY DIFFRACTIONr_bond_other_d0.0020.022024
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9313092
X-RAY DIFFRACTIONr_angle_other_deg0.80534667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2775287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02493
X-RAY DIFFRACTIONr_nbd_refined0.1850.2316
X-RAY DIFFRACTIONr_nbd_other0.2510.22433
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0770.21333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.561.51427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05122297
X-RAY DIFFRACTIONr_scbond_it1.73838
X-RAY DIFFRACTIONr_scangle_it2.784.5795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.226 69
Rwork0.187 1363

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