PDB-7seu: Crystal structure of E coli contaminant protein YncE co-purified ...

ID or keywords:

Entry

Database: PDB / ID: 7seu

Title

Crystal structure of E coli contaminant protein YncE co-purified with a plant protein

Components

PQQ-dependent catabolism-associated beta-propeller protein

Keywords

DNA BINDING PROTEIN /

DNA BINDING / YncE/P76116 / seven-bladed Beta-propeller

Function / homology

Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / WD40/YVTN repeat-like-containing domain superfamily /

Putative receptor

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Chai, L. / Zhu, P. / Chai, J. / Pang, C. / Andi, B. / McsWeeney, S. / Shanklin, J. / Liu, Q.

Funding support

United States, 2items

Citation

Journal: Crystals / Year: 2021
Title: AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement
Authors: Chai, L. / Zhu, P. / Chai, J. / Pang, C. / Andi, B. / McSweeney, S. / Shanklin, J. / Liu, Q.

History

Deposition	Oct 1, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7seu.cif.gz	501.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7seu.ent.gz	415.5 KB	Display	PDB format
PDBx/mmJSON format	7seu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/se/7seu ftp://data.pdbj.org/pub/pdb/validation_reports/se/7seu	HTTPS FTP

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Related structure data

Related structure data	7sevC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PQQ-dependent catabolism-associated beta-propeller protein

B: PQQ-dependent catabolism-associated beta-propeller protein

C: PQQ-dependent catabolism-associated beta-propeller protein

D: PQQ-dependent catabolism-associated beta-propeller protein

155 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PQQ-dependent catabolism-associated beta-propeller protein

defined by author&software
38.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PQQ-dependent catabolism-associated beta-propeller protein

defined by author&software
38.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: PQQ-dependent catabolism-associated beta-propeller protein

defined by author&software
38.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: PQQ-dependent catabolism-associated beta-propeller protein

defined by author&software
38.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.172, 147.270, 96.899
Angle α, β, γ (deg.)	90.000, 104.400, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 33 through 334 or resid 342 through 353))
2	1	(chain B and (resid 33 through 334 or resid 342 through 353))
3	1	(chain C and (resid 33 through 334 or resid 342 through 353))
4	1	(chain D and resid 33 through 353)

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	GLN	GLN	(chain A and (resid 33 through 334 or resid 342 through 353))	A	A	33 - 334	33 - 334
1	2	ALA	ALA	LEU	LEU	(chain A and (resid 33 through 334 or resid 342 through 353))	A	A	342 - 353	342 - 353
2	1	GLU	GLU	GLN	GLN	(chain B and (resid 33 through 334 or resid 342 through 353))	B	B	33 - 334	33 - 334
2	2	ALA	ALA	LEU	LEU	(chain B and (resid 33 through 334 or resid 342 through 353))	B	B	342 - 353	342 - 353
3	1	GLU	GLU	GLN	GLN	(chain C and (resid 33 through 334 or resid 342 through 353))	C	C	33 - 334	33 - 334
3	2	ALA	ALA	LEU	LEU	(chain C and (resid 33 through 334 or resid 342 through 353))	C	C	342 - 353	342 - 353
4	1	GLU	GLU	LEU	LEU	(chain D and resid 33 through 353)	D	D	33 - 353	33 - 353

#1: Protein	PQQ-dependent catabolism-associated beta-propeller protein / Putative receptor / Receptor / YncE family protein / YncE protein Mass: 38664.883 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A037YE18
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.38 Å³/Da / Density % sol: 48.23 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li2SO4, 0.1 M MES, pH 6.0, and 20% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 13, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 87600 / % possible obs: 95.9 % / Redundancy: 2.8 % / CC_1/2: 0.981 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.5→2.56 Å / Num. unique obs: 3604 / CC_1/2: 0.973

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PDB_EXTRACT	3.27	data extraction
DIALS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold AF-P76116-F1

Resolution: 2.5→48.61 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 30.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2559	4260	4.86 %
R_work	0.236	83340	-
obs	0.237	87600	88.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 122.31 Å² / B_iso mean: 46.581 Å² / B_iso min: 23.36 Å²

Refinement step

Cycle: final / Resolution: 2.5→48.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9852	0	0	272	10124
B_iso mean	-	-	-	39.26	-
Num. residues	-	-	-	-	1279

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6062	X-RAY DIFFRACTION	3.495	TORSIONAL
1	2	B	6062	X-RAY DIFFRACTION	3.495	TORSIONAL
1	3	C	6062	X-RAY DIFFRACTION	3.495	TORSIONAL
1	4	D	6062	X-RAY DIFFRACTION	3.495	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.5-2.53	0.3822	155	0.3218	2901	90
2.53-2.56	0.3478	131	0.3262	2736	89
2.56-2.59	0.3337	143	0.3243	2807	90
2.59-2.62	0.3548	135	0.312	2800	90

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	3.16	-0.9697	-1.2968	4.1355	-2.2166	4.9306	-0.0653	0.0845	-0.0824	-0.0817	-0.004	0.1583	-0.2997	-0.0048	0.0236	0.1449	0.0099	-0.0056	0.2499	0.0088	0.2983	0.7766	-6.1853	44.903
2	2.1363	-0.3981	0.2396	2.9405	0.1758	1.6905	-0.068	-0.3231	-0.2248	0.2974	0.0018	0.1267	0.0846	0.0382	0.0489	0.2181	0.0188	0.0076	0.175	0.0357	0.3565	-3.3238	-7.912	53.8264
3	3.4916	0.7986	1.19	4.0513	1.0793	5.3458	-0.2009	0.6192	-0.4329	-0.0694	0.4096	0.0971	0.944	0.202	0.1349	0.377	0.0256	0.1	0.341	0.032	0.4946	-21.2896	-13.2598	47.7928
4	3.3468	-0.1195	-0.8286	1.8431	-0.5924	3.6708	0.005	-0.3142	0.0324	0.1647	-0.0006	0.3611	-0.1769	-0.1392	0.0624	0.2242	0.0278	0.0511	0.2538	0.0417	0.4721	-21.4282	-0.5324	52.0596
5	3.2105	-1.1444	0.4861	2.6707	-0.6587	2.9736	0.0654	0.2648	0.2291	-0.1056	0.027	0.2608	0.1672	-0.256	-0.0657	0.2868	0.019	-0.0132	0.2797	0.0639	0.5161	-22.3745	7.9328	40.8258
6	2.7134	-0.1204	-0.4102	2.0545	0.7713	2.2222	0.0894	0.182	0.2623	-0.1361	-0.0426	0.1668	-0.2686	-0.1037	-0.0733	0.2567	-0.0032	0.0028	0.2298	0.0848	0.3963	-7.3218	8.6464	36.3912
7	2.6156	-1.6644	0.0533	4.0794	0.7603	4.8799	0.248	0.2886	-0.5091	0.1275	-0.2388	0.3809	0.6814	-0.3042	-0.0299	0.2503	0.0654	0.0048	0.2859	0.035	0.4004	-0.5159	-9.2681	34.7001
8	4.9392	-1.2533	-0.4764	3.4929	-0.6271	2.5614	0.0238	0.0827	-0.0963	-0.2338	-0.0571	0.0051	0.0423	-0.1536	-0.0189	0.1747	-0.0327	0.0096	0.2485	0.0671	0.3358	7.0594	-30.2647	51.691
9	1.9885	-0.0923	-0.5661	2.5801	-0.5451	2.5472	0.0011	0.1771	-0.1535	-0.195	0.0356	0.2843	0.0345	-0.4819	-0.0473	0.1393	-0.003	0.0182	0.1797	0.0448	0.3207	-1.7488	-29.3198	55.2324
10	5.0374	-0.9777	-0.3516	5.6248	-0.3503	6.2634	-0.5234	-0.3243	1.0428	0.2714	0.6297	-0.9369	-1.1279	0.5931	0.0917	0.4671	0.0549	-0.0937	0.4683	0.0003	0.721	3.501	-23.8802	73.4018
11	3.0816	-1.1395	0.4823	3.6583	-0.9014	3.3523	-0.0684	-0.3264	-0.0456	0.1795	0.1474	0.1992	-0.0801	-0.3874	-0.1003	0.244	-0.008	0.0442	0.2754	0.0787	0.329	-0.3979	-36.6998	73.3741
12	6.9363	-0.8345	-0.6079	3.0656	-0.0214	5.1396	0.3838	-0.4867	0.7414	0.7869	-0.0021	-0.3622	-0.3767	0.1606	-0.2148	0.4724	0.0324	-0.0815	0.2716	0.0714	0.5272	9.4353	-42.3372	78.8925
13	3.5596	-0.8192	-0.3711	2.0073	-0.0674	4.3267	0.255	-0.1647	-0.3871	-0.0734	-0.2048	-0.3861	0.3555	0.0305	-0.0878	0.2976	0.0085	-0.1145	0.3016	0.1025	0.6039	13.6178	-48.6762	67.9057
14	3.0793	-1.52	1.6643	2.386	-1.008	4.43	0.1039	0.1823	0.0699	-0.3425	-0.1578	-1.0358	0.211	0.5094	0.0086	0.2458	0.0159	0.054	0.297	0.0144	0.5615	16.781	-43.5124	56.3733
15	4.6194	1.1604	-0.0271	4.3262	-1.658	5.6329	0.1006	0.0666	0.9947	0.4298	-0.259	-0.675	-0.6236	0.7922	0.0524	0.3256	-0.0444	-0.0226	0.3326	0.0931	0.87	17.3717	-27.5754	53.0016
16	2.2954	-1.1699	0.1397	3.2279	-0.3496	5.9439	-0.1701	0.2315	-0.0442	0.0355	-0.0382	-0.1487	-0.1128	0.4191	0.0244	0.2204	-0.0436	0.0246	0.3429	-0.0344	0.2501	0.7863	4.8571	8.0679
17	3.3575	-0.4802	0.5421	3.1692	0.2151	4.0018	0.0583	0.2638	0.2364	-0.1539	-0.0225	-0.1464	-0.1418	0.4297	0.0341	0.2488	0.0085	-0.0112	0.3011	0.0199	0.2589	2.9367	6.2823	2.2009
18	3.4684	-1.4556	0.4474	2.7781	0.2992	5.7092	-0.009	0.8483	-0.1549	-0.6823	0.1135	-0.1855	0.0241	0.259	0.0107	0.3054	0.0652	0.0407	0.469	-0.0859	0.2858	0.203	0.426	-5.8265
19	5.1228	-0.7742	2.7272	3.3575	-0.175	5.5184	0.5804	0.0213	-0.8692	0.132	-0.0615	0.1056	0.8249	-0.4867	-0.5631	0.6039	-0.0621	-0.0221	0.409	-0.1588	0.456	-7.8157	-13.407	-2.4562
20	3.504	-0.3893	1.6287	0.4836	0.3985	3.4176	0.1668	0.5735	-0.7765	-0.6226	0.2139	-0.1912	0.8966	0.2694	-0.491	0.7321	0.1507	-0.0753	0.6035	-0.3052	0.7326	2.9168	-14.4338	-5.3309
21	3.2524	-1.1796	0.2946	1.6816	1.5932	2.7949	0.7361	0.9509	-1.6896	-0.3008	0.4678	-0.9947	1.5788	0.5683	0.8621	0.889	0.5808	-0.2884	0.6432	-0.5576	1.2201	10.8694	-21.3213	-0.1988
22	1.616	-0.6851	2.0364	2.1619	1.071	4.6435	0.7493	0.3731	-1.5216	0.3398	-0.0214	-0.4655	1.4557	0.5278	-0.5324	0.7501	0.2314	-0.2251	0.5354	-0.0986	1.0321	11.4949	-17.9558	14.0695
23	2.1694	0.5581	-0.0217	3.8114	-0.453	5.4789	0.1829	-0.198	-0.4166	0.0328	-0.2308	-0.348	0.1511	0.3097	0.0943	0.2649	0.068	-0.011	0.299	-0.0021	0.4269	9.2023	-6.9018	20.4682
24	5.3061	-0.2422	-0.8699	4.5135	-0.2996	5.7581	-0.1383	0.5363	-0.3202	0.1923	0.0177	0.1955	-0.072	-0.2913	0.059	0.2791	0.0486	-0.0084	0.1973	-0.0636	0.3237	0.6316	1.9918	15.5742
25	3.0512	0.7446	1.3324	2.6743	-0.0888	3.4267	-0.1096	-0.0373	0.1475	0.0236	0.0526	0.0176	-0.0749	-0.0586	-0.0221	0.2709	0.0575	-0.0078	0.2376	0.0015	0.2707	18.2841	-60.0413	5.0547
26	2.234	0.9407	-0.8225	2.7623	0.0933	2.7997	0.0492	-0.6562	0.3359	0.4365	-0.0671	0.4918	-0.0516	-0.6184	-0.118	0.5594	0.02	0.0368	0.6746	-0.0675	0.3417	12.7698	-56.4451	23.6682
27	2.9842	0.6833	0.6068	4.5749	0.0409	2.7146	0.2424	-0.877	0.4237	0.6453	-0.3938	-0.0544	-0.3123	-0.1919	-0.3954	0.6833	-0.03	-0.048	0.5578	-0.1513	0.4606	24.4345	-50.2321	29.7939
28	3.2279	3.136	-0.4723	3.5002	-0.0384	3.8783	-0.2135	-0.3691	1.5784	0.3832	-0.0756	0.5888	-0.7797	-0.4786	0.0611	0.624	0.0973	-0.1799	0.4504	-0.0806	0.7013	27.6424	-39.783	20.0555
29	4.8059	-1.697	2.0201	3.0582	-2.2329	5.6344	-0.8536	0.4619	1.0922	-0.2723	0.121	-0.0498	-1.003	0.3457	0.4869	0.6467	0.0006	-0.1419	0.3373	-0.0408	0.5891	29.6731	-38.045	7.7422
30	2.5956	0.1137	-1.0653	3.9884	0.3055	6.3496	-0.3374	0.81	0.4764	-0.5917	0.2227	0.333	-0.6252	-0.3766	0.2976	0.4264	-0.0433	-0.1127	0.3243	0.0563	0.4592	23.4028	-47.9717	0.9811

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 68 )	A	32 - 68
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 128 )	A	69 - 128
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 129 through 149 )	A	129 - 149
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 206 )	A	150 - 206
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 207 through 259 )	A	207 - 259
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 260 through 332 )	A	260 - 332
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 333 through 353 )	A	333 - 353
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 33 through 68 )	B	33 - 68
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 69 through 128 )	B	69 - 128
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 129 through 149 )	B	129 - 149
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 150 through 206 )	B	150 - 206
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 207 through 235 )	B	207 - 235
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 236 through 284 )	B	236 - 284
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 285 through 332 )	B	285 - 332
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 333 through 353 )	B	333 - 353
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 33 through 68 )	C	33 - 68
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 69 through 101 )	C	69 - 101
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 102 through 128 )	C	102 - 128
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 129 through 149 )	C	129 - 149
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 150 through 190 )	C	150 - 190
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 191 through 223 )	C	191 - 223
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 224 through 284 )	C	224 - 284
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 285 through 321 )	C	285 - 321
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 322 through 353 )	C	322 - 353
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 32 through 128 )	D	32 - 128
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 129 through 190 )	D	129 - 190
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 191 through 223 )	D	191 - 223
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 224 through 284 )	D	224 - 284
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 285 through 311 )	D	285 - 311
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 312 through 353 )	D	312 - 353

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