PDB-6dnv: Crystal Structure of Neisseria meningitidis DsbD n-terminal domai...

ID or keywords:

Entry

Database: PDB / ID: 6dnv

Title

Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the reduced form

Components

Thiol:disulfide interchange protein DsbD

Keywords

OXIDOREDUCTASE / disulphide reductase / Dsb proteins

Function / homology

Function and homology information

protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / cell redox homeostasis / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Neisseria meningitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.603 Å

Authors

Smith, R.P. / Heras, B. / Paxman, J.J.

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural and biochemical insights into the disulfide reductase mechanism of DsbD, an essential enzyme for neisserial pathogens.
Authors: Smith, R.P. / Mohanty, B. / Mowlaboccus, S. / Paxman, J.J. / Williams, M.L. / Headey, S.J. / Wang, G. / Subedi, P. / Doak, B.C. / Kahler, C.M. / Scanlon, M.J. / Heras, B.

History

Deposition	Jun 8, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 7, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6dnv.cif.gz	120.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6dnv_validation.pdf.gz	428.5 KB	Display	wwPDB validaton report
Full document	6dnv_full_validation.pdf.gz	429 KB	Display
Data in XML	6dnv_validation.xml.gz	15.3 KB	Display
Data in CIF	6dnv_validation.cif.gz	22.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dn/6dnv ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dnv	HTTPS FTP

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Related structure data

Related structure data	6dnlC 6dnuC 6dpsC C: citing same article (ref.)
Similar structure data	3h7q-d 4qyl-3 4n5u-d 2bc5-3 1c8p-d 3oj3-1 4rmr-d 5nhi-1 4q9c-d 2edy-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDCH7associated SAS data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thiol:disulfide interchange protein DsbD

B: Thiol:disulfide interchange protein DsbD

hetero molecules

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

1

A: Thiol:disulfide interchange protein DsbD

hetero molecules

defined by author
Evidence: gel filtration
14 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thiol:disulfide interchange protein DsbD

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

Unit cell

Length a, b, c (Å)	116.980, 116.980, 45.790
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-445- HOH
2	1	A-495- HOH

#1: Protein	Thiol:disulfide interchange protein DsbD / Protein-disulfide reductase / Disulfide reductase Mass: 13823.304 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: alpha14 / Gene: dsbD, NMO_1340 / Plasmid: pMCSG7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C6S7X6, protein-disulfide reductase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.27 Å³/Da / Density % sol: 62.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 2.5 M ammonium sulfate, 0.1 M Tris pH 9.1

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.9537 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection

Resolution: 1.603→101.308 Å / Num. obs: 47439 / % possible obs: 100 % / Redundancy: 10.6 % / B_iso Wilson estimate: 17.41 Å² / R_pim(I) all: 0.046 / R_rim(I) all: 0.15 / R_sym value: 0.143 / Net I/av σ(I): 4.2 / Net I/σ(I): 11.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
1.603-1.69	10.5	1.832	0.4	6907	0.594	1.927	1.832	100
1.69-1.79	10.8	1.048	0.7	6479	0.335	1.101	1.048	100
1.79-1.92	10.7	0.543	1.3	6123	0.174	0.571	0.543	100
1.92-2.07	10.7	0.292	2.5	5707	0.094	0.306	0.292	100
2.07-2.27	10.7	0.194	3.8	5232	0.062	0.204	0.194	100
2.27-2.53	10.7	0.14	5.3	4778	0.045	0.147	0.14	100
2.53-2.93	10.7	0.101	6.8	4230	0.032	0.106	0.101	100
2.93-3.58	10.6	0.089	6.6	3580	0.029	0.094	0.089	100
3.58-5.07	10.1	0.066	9.5	2812	0.022	0.069	0.066	100
5.07-41.726	10.7	0.046	13.2	1591	0.015	0.048	0.046	99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.22	data scaling
PHASER		phasing
PHENIX	dev_1951	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.603→41.726 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.26

	R_factor	Num. reflection	% reflection
R_free	0.1972	2256	4.76 %
R_work	0.1721	-	-
obs	0.1732	47425	99.95 %

Solvent computation

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

Displacement parameters

B_iso max: 79.97 Å² / B_iso mean: 25.0461 Å² / B_iso min: 8.06 Å²

Refinement step

Cycle: final / Resolution: 1.603→41.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1938	0	10	373	2321
B_iso mean	-	-	39.96	36.93	-
Num. residues	-	-	-	-	248

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2002
X-RAY DIFFRACTION	f_angle_d	1.059	2727
X-RAY DIFFRACTION	f_chiral_restr	0.049	280
X-RAY DIFFRACTION	f_plane_restr	0.005	367
X-RAY DIFFRACTION	f_dihedral_angle_d	12.97	723

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.6031-1.638	0.3275	146	0.2753	2817	2963
1.638-1.6761	0.2536	104	0.2553	2811	2915
1.6761-1.718	0.2596	123	0.2435	2833	2956
1.718-1.7644	0.2399	140	0.2275	2802	2942
1.7644-1.8164	0.2369	172	0.1961	2741	2913
1.8164-1.875	0.1918	144	0.1852	2810	2954
1.875-1.942	0.2022	144	0.1709	2787	2931
1.942-2.0198	0.1911	150	0.1582	2808	2958
2.0198-2.1117	0.1837	148	0.1653	2786	2934
2.1117-2.223	0.1872	130	0.1639	2821	2951
2.223-2.3623	0.2091	165	0.1708	2814	2979
2.3623-2.5446	0.1919	118	0.1728	2848	2966
2.5446-2.8007	0.1933	148	0.1757	2813	2961
2.8007-3.2058	0.2301	112	0.179	2865	2977
3.2058-4.0384	0.1609	154	0.1468	2867	3021
4.0384-41.7401	0.1828	158	0.1532	2946	3104

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	0.5516	-0.2476	-0.1608	0.461	-0.3031	0.43	0.0394	0.023	0.079	-0.1096	-0.0111	-0.0143	0.0173	0.0454	-0.0085	0.1388	0.0044	-0.0125	0.0505	0.0013	0.1034	242.931	90.0873	66.2906
2	0.073	-0.0074	-0.1599	0.0923	-0.0321	0.3984	-0.1001	-0.1119	0.0929	0.2141	0.0071	-0.1353	0.0102	0.179	-0.0061	0.1708	0.0392	-0.0146	0.0988	0.0152	0.1122	249.4807	84.6009	80.8557
3	0.3573	-0.0135	-0.0464	0.0649	0.0063	0.0274	0.1071	0.0837	0.12	-0.1962	-0.1349	-0.0687	0.0943	-0.0285	0.0302	0.2424	0.0463	-0.0247	0.103	0.009	0.1326	245.9375	87.6024	58.5695
4	0.1364	-0.0849	-0.2307	0.3518	0.0502	0.3151	0.0379	0.0263	0.0245	-0.1071	0.0134	0.0455	-0.0229	-0.1528	0.0022	0.1747	0.0035	-0.0182	0.0917	0.0055	0.1125	237.1412	89.8302	65.0286
5	0.0106	0.0022	0.0138	0.0035	0.0278	0.1572	0.0424	-0.1554	0.0059	0.3373	-0.105	-0.2828	-0.2646	0.325	-0.0002	0.4166	0.0261	-0.1338	0.2128	-0.0011	0.3234	233.2724	81.8665	82.484
6	0.0205	0.0144	-0.0311	0.1075	-0.0076	0.0617	0.11	0.1955	-0.048	-0.1616	0.0701	0.0903	0.0515	0.0537	0.0295	0.1479	-0.0353	-0.0602	0.1212	0.0021	0.2116	217.5748	81.9419	71.5947
7	0.6906	0.2669	-0.0499	0.2862	0.0209	0.013	0.1624	-0.1358	0.1126	0.0369	-0.0799	0.3819	0.1172	-0.0992	0.0101	0.1442	-0.0432	-0.0532	0.0734	-0.002	0.2013	215.8159	88.3555	75.0105
8	0.367	0.0538	0.1765	0.0172	0.0737	0.3086	-0.2046	0.3322	0.3325	-0.4833	0.1776	0.2539	-0.1209	0.0507	0.0941	0.4303	-0.1329	-0.1352	0.2491	0.0956	0.2814	215.0907	93.4919	59.503
9	0.6926	-0.0361	-0.4502	0.1789	-0.1762	0.5269	0.0402	-0.2885	0.2735	0.1133	-0.0922	0.2899	-0.1824	0.0235	-0.2812	0.1671	-0.0171	0.0338	0.0875	-0.0758	0.2626	219.3983	97.6326	80.4421
10	1.2887	0.1562	-0.2303	0.0807	-0.1137	0.1893	0.0563	-0.1992	0.4111	-0.0763	-0.0448	0.3583	-0.1373	-0.008	0.072	0.1746	-0.0072	-0.0116	0.0564	-0.0364	0.2621	214.952	93.3829	77.5661
11	0.0009	-0.0033	-0.0017	0.2205	-0.0273	0.0058	-0.1424	0.1006	0.1716	-0.0989	0.0398	0.0745	-0.0694	0.0009	-0.1304	0.6353	-0.1489	-0.2805	0.3088	0.1467	0.4704	207.7071	89.4016	53.8204
12	0.2636	-0.0546	-0.2081	0.5439	0.1127	0.2057	-0.0393	0.0757	0.0605	-0.1538	0.1603	0.1191	0.0729	-0.0379	0.1312	0.2082	-0.1049	-0.0501	0.1307	0.0254	0.1253	220.8145	88.5093	67.2386
13	0.4122	0.1686	-0.1066	0.0797	-0.0639	0.0603	0.0666	-0.3456	-0.0287	0.2015	-0.2334	-0.0476	-0.0693	-0.1482	-0.0163	0.1877	-0.025	-0.0265	0.1452	-0.003	0.1598	229.5346	89.742	80.1804
14	0.0144	-0.0279	0.0373	0.0572	-0.0729	0.0913	-0.0089	0.0724	0.0317	-0.0862	0.1414	-0.1443	0.0159	0.0574	0.1741	0.2361	-0.2527	-0.1079	0.1452	-0.0693	0.1115	220.1587	83.8151	62.435
15	0.4596	-0.1759	-0.5091	0.0732	0.1886	0.5667	-0.1273	-0.0747	0.0317	-0.2574	0.093	0.2357	-0.0404	0.1708	-0.082	0.1935	-0.0773	-0.0482	0.1727	0.0254	0.1489	212.4813	78.5509	63.0088

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 1 through 57 )	A	1 - 57
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 70 )	A	58 - 70
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 88 )	A	71 - 88
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 123 )	A	89 - 123
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 6 )	B	-1 - 6
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 7 through 18 )	B	7 - 18
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 19 through 38 )	B	19 - 38
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 39 through 51 )	B	39 - 51
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 52 through 65 )	B	52 - 65
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 80 )	B	66 - 80
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 81 through 88 )	B	81 - 88
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 89 through 99 )	B	89 - 99
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 100 through 107 )	B	100 - 107
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 108 through 114 )	B	108 - 114
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 115 through 123 )	B	115 - 123

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