PDB-8pks: Low resolution crystal structure of Keap1-456, a repeat fragment ...

ID or keywords:

Entry

Database: PDB / ID: 8pks

Title

Low resolution crystal structure of Keap1-456, a repeat fragment from the human Keap1 beta-propeller

Components

Kelch-like ECH-associated protein 1

Keywords

UNKNOWN FUNCTION / fragment / scaffold / beta propeller / globular / PknD

Function / homology

Function and homology information

regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Wouters, S.M.L.

Funding support

Belgium, 3items

Citation

Journal: To Be Published
Title: Fragment-based assembly of a symmetric protein scaffold
Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D.

History

Deposition	Jun 27, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pks.cif.gz	846.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8pks.ent.gz	629.2 KB	Display	PDB format
PDBx/mmJSON format	8pks.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pks_validation.pdf.gz	530.6 KB	Display	wwPDB validaton report
Full document	8pks_full_validation.pdf.gz	557.2 KB	Display
Data in XML	8pks_validation.xml.gz	68.6 KB	Display
Data in CIF	8pks_validation.cif.gz	94.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/8pks ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pks	HTTPS FTP

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Related structure data

Related structure data	8pkqC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1)

Deposited unit

A: Kelch-like ECH-associated protein 1

B: Kelch-like ECH-associated protein 1

C: Kelch-like ECH-associated protein 1

D: Kelch-like ECH-associated protein 1

E: Kelch-like ECH-associated protein 1

F: Kelch-like ECH-associated protein 1

G: Kelch-like ECH-associated protein 1

H: Kelch-like ECH-associated protein 1

I: Kelch-like ECH-associated protein 1

J: Kelch-like ECH-associated protein 1

K: Kelch-like ECH-associated protein 1

L: Kelch-like ECH-associated protein 1

M: Kelch-like ECH-associated protein 1

N: Kelch-like ECH-associated protein 1

222 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kelch-like ECH-associated protein 1

B: Kelch-like ECH-associated protein 1

defined by author&software
Evidence: gel filtration
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Kelch-like ECH-associated protein 1

D: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Kelch-like ECH-associated protein 1

F: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Kelch-like ECH-associated protein 1

H: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Kelch-like ECH-associated protein 1

J: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Kelch-like ECH-associated protein 1

L: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Kelch-like ECH-associated protein 1

N: Kelch-like ECH-associated protein 1

defined by author&software
31.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.846, 220.962, 248.750
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: Protein	Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19 Mass: 15843.566 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14145
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.62 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / Details: 0.1 M Bis-Tris pH 5.5, 2 M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 20, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.54 Å / Num. obs: 81023 / % possible obs: 100 % / Redundancy: 9.3 % / B_iso Wilson estimate: 57.47 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.026 / R_rim(I) all: 0.08 / Χ²: 1.02 / Net I/σ(I): 23.1
Reflection shell	Resolution: 2.7→2.76 Å / % possible obs: 100 % / Redundancy: 9.9 % / R_merge(I) obs: 0.773 / Num. measured all: 44335 / Num. unique obs: 4486 / CC_1/2: 0.839 / R_pim(I) all: 0.258 / R_rim(I) all: 0.815 / Χ²: 0.99 / Net I/σ(I) obs: 3.2

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→48.54 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2591	4032	4.98 %
R_work	0.2138	76991	-
obs	0.2161	81023	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 70.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→48.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14764	0	0	305	15069

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0049	15074
X-RAY DIFFRACTION	f_angle_d	0.814	20542
X-RAY DIFFRACTION	f_chiral_restr	0.057	2269
X-RAY DIFFRACTION	f_plane_restr	0.0132	2680
X-RAY DIFFRACTION	f_dihedral_angle_d	16.758	5128

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.63	0.4136	132	0.3067	2558	X-RAY DIFFRACTION	99.96
2.63-2.66	0.3638	136	0.3007	2585	X-RAY DIFFRACTION	99.93
2.66-2.7	0.3647	116	0.2924	2627	X-RAY DIFFRACTION	99.96
2.7-2.73	0.3477	141	0.27	2662	X-RAY DIFFRACTION	100
2.73-2.77	0.3374	133	0.2603	2627	X-RAY DIFFRACTION	100
2.77-2.81	0.3382	127	0.2443	2564	X-RAY DIFFRACTION	100
2.81-2.85	0.2657	137	0.2449	2630	X-RAY DIFFRACTION	100
2.85-2.9	0.3404	130	0.247	2654	X-RAY DIFFRACTION	100
2.9-2.94	0.2932	148	0.2455	2639	X-RAY DIFFRACTION	100
2.94-2.99	0.2738	143	0.2502	2552	X-RAY DIFFRACTION	100
2.99-3.05	0.3086	155	0.2572	2620	X-RAY DIFFRACTION	100
3.05-3.11	0.3493	126	0.2679	2696	X-RAY DIFFRACTION	100
3.11-3.17	0.3581	145	0.2492	2584	X-RAY DIFFRACTION	100
3.17-3.24	0.2633	131	0.2312	2616	X-RAY DIFFRACTION	99.96
3.24-3.31	0.2617	142	0.2338	2671	X-RAY DIFFRACTION	100
3.31-3.4	0.2918	133	0.2342	2620	X-RAY DIFFRACTION	100
3.4-3.49	0.2954	133	0.2335	2633	X-RAY DIFFRACTION	99.96
3.49-3.59	0.3051	135	0.2295	2691	X-RAY DIFFRACTION	100
3.59-3.71	0.232	131	0.2172	2633	X-RAY DIFFRACTION	99.93
3.71-3.84	0.2767	141	0.2071	2659	X-RAY DIFFRACTION	100
3.84-3.99	0.2451	129	0.1919	2640	X-RAY DIFFRACTION	99.82
3.99-4.18	0.2249	158	0.1734	2652	X-RAY DIFFRACTION	100
4.18-4.39	0.1987	143	0.1533	2662	X-RAY DIFFRACTION	100
4.4-4.67	0.2027	148	0.1656	2726	X-RAY DIFFRACTION	100
4.67-5.03	0.2343	152	0.1748	2643	X-RAY DIFFRACTION	100
5.03-5.54	0.22	154	0.1799	2687	X-RAY DIFFRACTION	100
5.54-6.34	0.277	144	0.2255	2743	X-RAY DIFFRACTION	100
6.34-7.98	0.2582	150	0.2485	2780	X-RAY DIFFRACTION	100
7.98-48.54	0.2298	139	0.224	2937	X-RAY DIFFRACTION	99.61

Refinement TLS params.

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

ID	L11 (°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)
1	4.00514682088	-0.541235860533	-0.474428307415	3.6101235317	-0.911625889163	4.55448058303	-0.383075230145	-0.235071287621	0.33004670783	0.340571554082	0.224508432213	-0.317374501906	-0.211913858162	0.147358823554	0.1164871457	0.379465615821	0.153717873463	-0.127682159811	0.392178510779	-0.0976316436333	0.46650115563	8.90963872912	0.249325591082	37.6349275538
2	4.59524570232	-0.406451393038	0.456981386231	3.43537505744	-0.277436459814	2.89739515051	-0.484882846763	-0.00187496604146	0.431068907166	0.352570568561	0.510599480496	-0.0106857597498	-0.247779340884	-0.309821299177	-0.00975160859003	0.415097898093	0.142757426726	-0.0620675515471	0.369909684074	-0.0225796514356	0.383667390419	-7.48906213107	4.11546004505	31.7389619382
3	3.45793204729	-0.735472011705	-0.293512783703	3.84958295348	0.0957112117193	4.2948474838	0.112142763652	0.0947146828052	0.0805966565109	-0.0804095943705	0.010138724794	-0.0802017302186	-0.0767188908057	-0.199369259863	-0.114450047692	0.260526266315	-0.0356722563902	-0.0202473270384	0.288288698364	-0.0204428863805	0.334746717965	-12.6795784411	-7.125128957	0.315647864782
4	3.41449241554	-2.36540181736	0.0646895049458	5.20120719564	-0.133774825461	3.52561662952	-0.200877770883	-0.0846845098776	-0.60552684248	0.301841648492	0.134092544609	0.500469301781	0.31122212274	-0.411642156015	0.0459808855792	0.435325749719	-0.119333610547	0.0187346693058	0.343677579812	-0.0171895108637	0.480162692163	-17.2570490928	-24.1617603851	0.508747497597
5	2.12548761168	-0.362953251794	-0.814272874056	1.58204447465	0.777747679376	3.5101654909	-0.0379824665444	0.0760463476834	-0.382388119815	0.138516850887	-0.157350077068	0.262442414807	0.407962360409	-0.0926768776891	0.174820422973	0.832328318386	-0.0920319175804	0.00282880317389	0.299233787623	-0.0710546533178	0.532389134384	-0.948752790424	-55.0497644169	-20.967374948
6	2.99177814559	-0.593573326769	-0.643045045637	3.04529449992	-0.0257762797427	3.22623020109	0.0211044079854	-0.278693987908	0.0517420954319	-0.11917672124	0.0369937251944	-0.0866073254941	0.174471154892	0.297264616444	-0.0521661137283	0.570333784826	-0.0512784373166	-0.0478908501627	0.285858096931	-0.0450734688344	0.400026263838	5.59272374572	-42.1907464203	-10.9711910735
7	4.91754719057	-0.207237475409	-0.109536583123	5.47882297265	1.25022571142	5.61896579438	-0.490923084232	0.963105342699	-0.0678589658461	0.113226106304	0.420255795442	-0.206183495474	0.0431809345389	0.752104708276	0.0528150514178	0.358793114993	-0.0179067118848	0.0358606158625	0.651475385857	-0.0499850089326	0.41158747728	-11.5706430528	36.045810024	32.8096172117
8	4.30441062912	0.321702268304	-0.022747433756	2.38520031616	0.147596573189	5.62738189376	-0.440024132617	0.356640618971	0.0200792511658	0.0751155622481	0.130744438551	0.253736824731	-0.0621710585228	-0.594236603925	0.218170957577	0.373272661046	0.0801695639773	-0.00896552567272	0.405835719527	-0.059695087806	0.546798786052	-27.7707180489	39.9428652442	38.9478009911
9	3.507413502	-0.230051894072	0.881124472979	5.87786730942	-1.27873413827	3.76949791381	0.0471483905331	0.245824038452	-0.189021586675	-0.45961681041	-0.114279390306	-0.121544042467	0.292925745474	-0.167277678047	0.0770447990494	0.554322220239	0.0947697758698	0.032877072521	0.241516435044	-0.0659107988995	0.446573939432	2.10376282323	-59.8943367178	-61.4847874395
10	3.06821217704	-1.27925189157	0.154131560903	4.7446475172	-1.83602991499	5.76232251907	0.0564706516242	0.132159367757	0.224509877064	0.110783660997	-0.574448852009	-1.13123451045	0.0586843269752	0.669493477837	0.377216759178	0.455285658719	0.0726287935239	-0.0374041259215	0.402886295925	0.12956865766	0.685531540584	13.3977689302	-56.5643033089	-48.6426456232
11	1.08858683397	0.677759639239	-0.205118805318	2.22692103107	0.673544625258	3.46154859746	-0.128570041069	0.307662473043	-0.0347308051187	-0.269479754192	0.240796266833	-0.335354377596	-0.314250795841	1.31651576342	0.0359388488446	0.506173609558	-0.326335997729	0.066326604057	1.20871351674	-0.0868570187309	0.528705439175	-4.30039625175	-91.2391870448	-72.2230715442
12	2.33130163387	1.23910045005	0.181468144745	5.04050654662	-0.48780443856	5.73754219153	-0.161664721573	0.11241606375	0.120357663495	0.00932765245067	-0.014711900626	0.141748096503	-0.219215373761	-0.333239010205	0.167935103401	0.264757303514	-0.096328404687	0.0478026309642	0.463662724532	-0.0630805369365	0.386950958878	-15.8709959401	-87.8255602319	-59.4513690926
13	2.26956479095	0.611389906415	-0.0254833220653	2.05669978917	0.687247850772	5.1633257065	-0.0803755946547	0.0783946494119	0.305954122439	-0.542097787764	0.0792962247904	0.281912973947	-1.16467910682	0.250338243377	0.049065405637	0.991013185669	-0.247550716296	-0.0868962344655	0.734310096038	-0.0744735046472	0.50680963672	-18.5551772532	-88.8317147338	-100.693722129
14	3.16323432807	1.09929586872	0.634602484157	3.67548947551	2.12886347268	3.32717775049	0.263353799603	0.107431930002	0.0570515724377	-0.0400181977132	0.0805197380022	-0.355271398368	-0.767416546154	1.61097393336	-0.0351846355155	0.602447319637	-0.324090634002	-0.00511826699197	1.1581159807	-0.0603149381708	0.495981072904	-11.3246671843	-100.916260544	-111.319855149

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	(chain 'A' and resid 3 through 143)	A	A	3 - 143	1 - 139
2	2	(chain 'B' and resid 4 through 143)	B	B	4 - 143	1 - 138
3	3	(chain 'C' and resid 5 through 143)	C	C	5 - 143	1 - 139
4	4	(chain 'D' and resid 4 through 143)	D	D	4 - 143	1 - 138
5	5	(chain 'E' and resid 5 through 143)	E	E	5 - 143	1 - 139
6	6	(chain 'F' and resid 4 through 143)	F	F	4 - 143	1 - 140
7	7	(chain 'G' and resid 3 through 143)	G	G	3 - 143	1 - 139
8	8	(chain 'H' and resid 4 through 143)	H	H	4 - 143	1 - 140
9	9	(chain 'I' and resid 4 through 143)	I	I	4 - 143	1 - 140
10	10	(chain 'J' and resid 4 through 143)	J	J	4 - 143	1 - 140
11	11	(chain 'K' and resid 4 through 143)	K	K	4 - 143	1 - 140
12	12	(chain 'L' and resid 3 through 143)	L	L	3 - 143	1 - 141
13	13	(chain 'M' and resid 4 through 143)	M	M	4 - 143	1 - 134
14	14	(chain 'N' and resid 4 through 143)	N	N	4 - 143	1 - 140

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