PDB-7pq8: Crystal structure of Campylobacter jejuni DsbA1

ID or keywords:

Entry

Database: PDB / ID: 7pq8

Title

Crystal structure of Campylobacter jejuni DsbA1

Components

Thiol:disulfide interchange protein DsbA

Keywords

OXIDOREDUCTASE / disulfide bond / thioredoxin fold / periplasmic / posttranslational modification

Function / homology

Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / isomerase activity / Thioredoxin-like superfamily / oxidoreductase activity / Thiol:disulfide interchange protein DsbA

Function and homology information

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.329 Å

Authors

Orlikowska, M. / Bocian-Ostrzycka, K.M. / Banas, A.M. / Jagusztyn-Krynicka, E.K.

Funding support

Poland, 2items

Citation

Journal: Int J Mol Sci / Year: 2021
Title: Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.
Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / ...

History

Deposition	Sep 16, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 5, 2022	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7pq8.cif.gz	98.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7pq8.ent.gz	71.5 KB	Display	PDB format
PDBx/mmJSON format	7pq8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7pq8_validation.pdf.gz	707.4 KB	Display	wwPDB validaton report
Full document	7pq8_full_validation.pdf.gz	708.2 KB	Display
Data in XML	7pq8_validation.xml.gz	12.8 KB	Display
Data in CIF	7pq8_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pq/7pq8 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pq8	HTTPS FTP

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Related structure data

Related structure data	7pq7SC 7pqfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ris-d 7pq7-1 5h87-2 2riu-d 3ovx-2 5h88-1 5lr6-2 5o20-d 1y9q-d 5zbe-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: Thiol:disulfide interchange protein DsbA

hetero molecules

23.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	34.489, 57.670, 93.778
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Thiol:disulfide interchange protein DsbA Mass: 23396.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_ ...Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_05085, FVY60_01390, FW488_04080, FZ445_05615, FZ732_06740, G3M94_001567, GFF90_03350, GMG47_05310, GNO00_06010, GXA88_04885, GXS76_000973, GZ489_001237, GZ502_000952 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A1J6PBD5
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.12 Å³/Da / Density % sol: 41.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.12 M Ethylene glycols, 0.1M Tris/BICINE pH 8.5, 50 % v/v Precipitant Mix 1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.329→48.86 Å / Num. obs: 51341 / % possible obs: 97.8 % / Redundancy: 3.78 % / CC_1/2: 0.99 / Net I/σ(I): 8.94
Reflection shell	Resolution: 1.33→1.41 Å / Num. unique obs: 12965 / CC_1/2: 0.65

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7PQ7

7pq7

Resolution: 1.329→46.889 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.402 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2192	1117	2.582 %
R_work	0.1759	42145	-
all	0.177	-	-
obs	-	43262	98.556 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 14.025 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.905 Å²	0 Å²	-0 Å²
2-	-	0.426 Å²	0 Å²
3-	-	-	0.479 Å²

Refinement step

Cycle: LAST / Resolution: 1.329→46.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1549	0	13	298	1860

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1688
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1558
X-RAY DIFFRACTION	r_angle_refined_deg	1.754	1.636	2286
X-RAY DIFFRACTION	r_angle_other_deg	1.574	1.583	3605
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.235	5	209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.966	24.891	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.042	15	295
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.018	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	209
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1987
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	413
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	379
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	1444
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	824
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	721
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	195
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.267	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.302	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.139	0.2	43
X-RAY DIFFRACTION	r_mcbond_it	0.773	0.958	812
X-RAY DIFFRACTION	r_mcbond_other	0.769	0.955	811
X-RAY DIFFRACTION	r_mcangle_it	1.229	1.434	1029
X-RAY DIFFRACTION	r_mcangle_other	1.229	1.437	1030
X-RAY DIFFRACTION	r_scbond_it	1.229	1.158	876
X-RAY DIFFRACTION	r_scbond_other	1.229	1.161	877
X-RAY DIFFRACTION	r_scangle_it	1.919	1.662	1257
X-RAY DIFFRACTION	r_scangle_other	1.918	1.665	1258
X-RAY DIFFRACTION	r_lrange_it	3.921	13.556	2066
X-RAY DIFFRACTION	r_lrange_other	3.596	12.533	1979

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.329-1.364	0.28	79	0.251	3009	0.252	3181	0.801	0.826	97.0764	0.24
1.364-1.401	0.255	79	0.23	2983	0.231	3137	0.874	0.884	97.6092	0.214
1.401-1.442	0.28	77	0.213	2875	0.215	3032	0.872	0.911	97.3615	0.194
1.442-1.486	0.267	75	0.198	2835	0.2	2934	0.888	0.927	99.182	0.176
1.486-1.535	0.234	72	0.189	2730	0.19	2847	0.924	0.935	98.4194	0.166
1.535-1.589	0.229	71	0.175	2664	0.176	2784	0.93	0.944	98.2399	0.152
1.589-1.649	0.198	69	0.173	2599	0.174	2704	0.944	0.949	98.6686	0.152
1.649-1.716	0.24	64	0.181	2444	0.182	2551	0.919	0.942	98.3144	0.159
1.716-1.792	0.245	64	0.176	2390	0.177	2478	0.924	0.945	99.0315	0.157
1.792-1.879	0.189	60	0.16	2289	0.161	2371	0.94	0.955	99.0721	0.144
1.879-1.981	0.161	58	0.168	2185	0.168	2263	0.957	0.951	99.1162	0.153
1.981-2.101	0.219	55	0.168	2083	0.17	2150	0.936	0.955	99.4419	0.158
2.101-2.245	0.224	52	0.154	1960	0.155	2029	0.941	0.967	99.1621	0.15
2.245-2.425	0.161	48	0.155	1798	0.155	1892	0.971	0.963	97.5687	0.154
2.425-2.656	0.234	45	0.166	1702	0.168	1760	0.932	0.951	99.2614	0.169
2.656-2.968	0.223	41	0.174	1542	0.175	1589	0.924	0.948	99.6224	0.178
2.968-3.425	0.231	37	0.173	1380	0.174	1420	0.948	0.958	99.7887	0.182
3.425-4.189	0.192	31	0.156	1187	0.157	1220	0.96	0.968	99.8361	0.178
4.189-5.9	0.209	24	0.186	922	0.187	967	0.958	0.962	97.8283	0.229
5.9-46.889	0.33	16	0.226	568	0.229	586	0.874	0.941	99.6587	0.271

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	0.2356	0.0846	0.0235	0.2338	0.1193	0.551	0.0063	0.0077	-0.0229	0.0048	-0.023	0.0066	-0.0298	0.0041	0.0167	0.035	-0	-0.0044	0.0066	-0.0061	0.0152	9.5778	-0.3063	-6.4771
2	0.4233	0.0881	0.0469	0.131	0.1361	0.455	0.0039	0.0047	-0.0171	0.0032	-0.0037	0.0057	-0.0108	0.0163	-0.0002	0.038	-0.0012	-0.0038	0.0017	-0.0011	0.0163	10.4703	-0.3089	-6.6187

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 193
2	X-RAY DIFFRACTION	2	ALL	A	401 - 698

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