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- PDB-3zgd: crystal structure of a KEAP1 mutant -

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Basic information

Entry
Database: PDB / ID: 3zgd
Titlecrystal structure of a KEAP1 mutant
ComponentsKELCH-LIKE ECH-ASSOCIATED PROTEIN 1
KeywordsTRANSCRIPTION / CRYSTAL CONTACT ENGINEERING
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
ACETATE ION / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHoerer, S. / Reinert, D. / Ostmann, K. / Hoevels, Y. / Nar, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystal-Contact Engineering to Obtain a Crystal Form of the Kelch Domain of Human Keap1 Suitable for Ligand-Soaking Experiments.
Authors: Horer, S. / Reinert, D. / Ostmann, K. / Hoevels, Y. / Nar, H.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
B: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,29513
Polymers67,6822
Non-polymers61311
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-18.2 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.720, 75.770, 202.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.003531, -0.8684, -0.4958), (-1, -0.003151, -0.001602), (-0.000171, 0.4958, -0.8685)
Vector: 16.39, 0.5974, 41.13)

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Components

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


Mass: 33840.848 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN, RESIDUES 321-609 / 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) / Variant (production host): PLYSS / References: UniProt: Q14145
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 4.44 Å3/Da / Density % sol: 72.3 % / Description: NONE
Crystal growpH: 5
Details: 4.0 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.002
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 1.98→38 Å / Num. obs: 82414 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 42.42 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.9
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
CDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U6D

1u6d


Resolution: 1.98→37.86 Å / Cor.coef. Fo:Fc: 0.9658 / Cor.coef. Fo:Fc free: 0.9585 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.089
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5099. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5099. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 4014 4.91 %RANDOM
Rwork0.1643 ---
obs0.1651 81695 99.91 %-
Displacement parametersBiso mean: 44.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.9823 Å20 Å20 Å2
2--2.6788 Å20 Å2
3----0.6965 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: LAST / Resolution: 1.98→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 41 667 5080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084530HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986163HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1489SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes699HARMONIC5
X-RAY DIFFRACTIONt_it4530HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion14.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
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_contact5536SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 280 4.72 %
Rwork0.1867 5650 -
all0.1871 5930 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0573-0.14520.03061.4434-0.27050.8453-0.02270.072-0.04420.04460.02710.13060.1298-0.1063-0.00450.0008-0.01720.0563-0.07270.0254-0.0688-3.2189-9.626638.5897
21.3725-0.1586-0.03150.8960.0321.08550.01780.05770.14270.0237-0.0343-0.05-0.09240.03430.0166-0.0652-0.01420.0123-0.01120.0892-0.055910.076515.825612.0448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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