PDB-6wed: Copper-bound E44Q variant of Campylobacter jejuni P19

ID or keywords:

Entry

Database: PDB / ID: 6wed

Title

Copper-bound E44Q variant of Campylobacter jejuni P19

Components

Uncharacterized protein

Keywords

TRANSPORT PROTEIN / iron transport / copper cofactor / periplasmic

Function / homology

Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / metal ion binding / COPPER (II) ION / Iron transporter

Function and homology information

Biological species

Campylobacter jejuni subsp. jejuni serotype O:23/36 (Campylobacter)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Chan, A.C. / Murphy, M.E.

Funding support

Canada, 1items

Citation

Journal: Metallomics / Year: 2020
Title: A copper site is required for iron transport by the periplasmic proteins P19 and FetP.
Authors: Chan, A.C.K. / Lin, H. / Koch, D. / Grass, G. / Nies, D.H. / Murphy, M.E.P.

History

Deposition	Apr 2, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wed.cif.gz	193.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6wed.ent.gz	156.8 KB	Display	PDB format
PDBx/mmJSON format	6wed.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6wed_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6wed_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6wed_validation.xml.gz	15.9 KB	Display
Data in CIF	6wed_validation.cif.gz	23 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/6wed ftp://data.pdbj.org/pub/pdb/validation_reports/we/6wed	HTTPS FTP

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Related structure data

Related structure data	5i0vC 5i0wC 5i0xC 5i0yC 6weeC 6wefC 3lzlS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6wee-3 6wef-2 6wef-5 6wef-1 3nrq-d 6wee-1 3lzr-d 6wee-2 5i0v-d 5i0w-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

35.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	55.347, 73.336, 78.957
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-426- HOH

#1: Protein	Uncharacterized protein Mass: 17589.875 Da / Num. of mol.: 2 / Mutation: E44Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter) Strain: 81-176 / Gene: CJJ81176_1650 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3PA01
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 45.99 % / Mosaicity: 1.087 ° / Mosaicity esd: 0.012 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M BisTris pH 6.5, 20% PEG 550, and 40 mM CaCl2 dihydrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 22, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 25790 / % possible obs: 99.2 % / Redundancy: 6.7 % / R_merge(I) obs: 0.086 / R_pim(I) all: 0.035 / R_rim(I) all: 0.093 / Χ²: 1.104 / Net I/σ(I): 8 / Num. measured all: 173279

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	3.5	0.515	1138	0.85	0.294	0.598	0.726	88.8
1.93-1.97	4.4	0.521	1242	0.873	0.271	0.591	0.758	97.4
1.97-2.01	6.1	0.45	1265	0.918	0.198	0.493	0.738	99.2
2.01-2.05	6.8	0.391	1277	0.95	0.16	0.423	0.762	99.5
2.05-2.09	7	0.341	1274	0.968	0.138	0.368	0.762	99.5
2.09-2.14	7	0.303	1280	0.964	0.121	0.327	0.815	99.7
2.14-2.19	7	0.288	1286	0.968	0.115	0.311	0.837	99.9
2.19-2.25	7.1	0.249	1266	0.975	0.1	0.268	0.874	99.9
2.25-2.32	7.1	0.211	1279	0.983	0.085	0.228	0.903	99.9
2.32-2.39	7.1	0.188	1284	0.986	0.075	0.203	0.889	99.9
2.39-2.48	7.1	0.171	1283	0.986	0.068	0.185	0.876	100
2.48-2.58	7.1	0.152	1290	0.989	0.06	0.163	0.988	100
2.58-2.7	7.1	0.132	1310	0.992	0.053	0.143	1.015	100
2.7-2.84	7.1	0.109	1298	0.994	0.044	0.117	1.101	100
2.84-3.02	7.2	0.094	1298	0.995	0.038	0.101	1.24	100
3.02-3.25	7.1	0.078	1302	0.996	0.031	0.085	1.405	100
3.25-3.58	7.1	0.064	1325	0.997	0.026	0.07	1.678	100
3.58-4.09	7.1	0.056	1311	0.997	0.022	0.06	1.739	100
4.09-5.16	7	0.048	1351	0.998	0.019	0.052	1.822	100
5.16-50	6.6	0.042	1431	0.999	0.018	0.046	1.562	99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
DENZO		data reduction
HKL-3000		data scaling
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LZL

3lzl

Resolution: 1.9→28.506 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.83

	R_factor	Num. reflection	% reflection
R_free	0.2218	1999	7.78 %
R_work	0.1739	-	-
obs	0.1776	25709	98.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 98.86 Å² / B_iso mean: 34.403 Å² / B_iso min: 11.81 Å²

Refinement step

Cycle: final / Resolution: 1.9→28.506 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2452	0	7	256	2715
B_iso mean	-	-	58.09	35.64	-
Num. residues	-	-	-	-	314

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 (%)
1.9003-1.9478	0.3076	118	0.2703	1513	90
1.9478-2.0004	0.2781	151	0.2309	1660	98
2.0004-2.0593	0.2504	138	0.1978	1682	100
2.0593-2.1257	0.2563	138	0.187	1683	100
2.1257-2.2017	0.2349	155	0.1966	1673	100
2.2017-2.2898	0.2418	141	0.1943	1691	100
2.2898-2.3939	0.2964	137	0.1843	1682	100
2.3939-2.5201	0.2576	143	0.1885	1707	100
2.5201-2.6779	0.2219	143	0.1856	1694	100
2.6779-2.8844	0.2185	145	0.1822	1699	100
2.8844-3.1744	0.2523	141	0.1887	1719	99
3.1744-3.6329	0.2158	145	0.156	1724	100
3.6329-4.574	0.1674	151	0.1356	1744	100
4.574-28.506	0.1895	153	0.1642	1839	99

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	0.0629	-0.0594	-0.077	0.1653	0.0078	0.3065	-0.0231	-0.0908	0.1521	-0.0538	0.0572	-0.1544	0.1433	0.0909	-0.0039	0.1288	0.0135	-0.0187	0.1884	-0.038	0.2211	27.0469	11.3017	33.9388
2	0.8266	0.3257	0.2666	0.2394	-0.0363	0.2354	0.4792	-0.5414	0.1726	-0.0627	-0.0408	0.2511	-0.2341	-0.2032	0.0714	0.2196	0.1095	-0.0253	0.2384	-0.133	0.3604	10.9569	25.2021	33.7811
3	0.5308	0.1881	0.2148	0.5471	0.3366	0.3731	-0.0533	-0.1247	0.054	-0.0655	-0.0336	-0.0282	-0.082	0.0473	-0.0011	0.13	0.0292	0.0199	0.1482	0.005	0.1727	21.7005	12.7474	28.1805
4	0.2825	-0.0466	0.1203	0.6774	0.6271	0.6056	-0.0312	-0.2495	0.1808	0.0312	-0.0962	0.2061	0.0295	-0.0041	-0.1089	0.1836	0.0189	0.0145	0.233	-0.0401	0.1953	15.9545	14.9657	35.0991
5	0.0819	0.0189	0.0668	0.6779	-0.0888	0.0959	0.0162	-0.6261	0.2404	0.7129	0.0245	0.5932	0.3929	0.118	0.0229	0.2662	0.0159	0.0968	0.449	-0.0676	0.2737	10.0772	14.4467	48.5034
6	0.5717	-0.1611	0.035	1.3228	-0.1652	0.3929	-0.0616	-0.0121	-0.1216	-0.2033	0.0451	-0.0107	0.2092	-0.0451	0.0307	0.1284	-0.0107	0.007	0.1452	-0.0181	0.1775	20.0116	5.2122	20.2314
7	0.275	-0.0833	-0.2386	-0.0061	0.0706	0.5216	-0.2927	-0.2816	-0.0587	-0.0022	0.069	-0.033	0.0747	0.2558	-0.0627	0.1478	0.0371	-0.044	0.3017	-0.0241	0.2049	22.0626	9.5726	41.2346
8	2.1395	-0.2403	0.0461	0.1943	0.0807	0.0842	-0.2238	0.5531	0.2001	0.1228	-0.1229	-0.0326	-0.6689	0.512	-0.2675	0.4671	-0.0889	-0.0985	0.256	0.1547	0.286	25.1494	26.2668	3.1077
9	0.0378	-0.0842	0.0052	0.1417	0.0279	0.1151	0.1636	0.7012	-0.0175	0.2197	-0.3001	-0.0744	0.3328	-0.0175	-0.0072	0.2679	-0.0176	-0.0288	0.3358	-0.043	0.2668	15.8624	6.7869	2.2283
10	0.6114	-0.046	-0.4306	0.1219	-0.3372	0.5577	-0.0314	0.2587	0.1126	-0.0381	-0.0122	0.0921	-0.2937	0.0813	0.0011	0.2507	0.0295	-0.0501	0.1637	0.0285	0.2087	20.4666	22.4833	8.5383
11	0.2447	-0.2783	0.785	0.2278	-0.6154	0.3069	-0.0264	0.2009	0.1108	0.0513	-0.1228	0.0232	-0.0494	0.1217	-0.0632	0.2278	0.0517	-0.0498	0.2622	0.0132	0.1839	15.1785	19.8319	-2.4765
12	1.2426	0.0406	0.4261	0.0196	0.0244	0.1816	0.0713	-0.356	0.2559	-0.1877	-0.2833	0.2097	-0.6203	-0.5765	0.0371	0.4322	0.128	-0.0856	0.1587	-0.0531	0.2855	14.8966	29.0131	24.1726
13	0.1108	-0.1901	0.0225	0.3199	0.1453	0.5615	-0.2942	0.3585	0.1407	0.3868	-0.0571	0.0309	0.0922	0.8562	0.0034	0.3104	0.0148	-0.0754	0.303	0.0671	0.3084	20.3962	26.0381	-4.6151

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 2 through 22 )	A	2 - 22
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 35 )	A	23 - 35
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 74 )	A	36 - 74
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 100 )	A	75 - 100
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 112 )	A	101 - 112
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 145 )	A	113 - 145
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 146 through 158 )	A	146 - 158
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 22 )	B	2 - 22
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 23 through 35 )	B	23 - 35
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 36 through 74 )	B	36 - 74
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 75 through 122 )	B	75 - 122
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 145 )	B	123 - 145
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 146 through 158 )	B	146 - 158

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