PDB-8s68: Low pH (5.5) as-isolated MSOX movie series dataset 20 of the copp...

ID or keywords:

Entry

Database: PDB / ID: 8s68

Title

Low pH (5.5) as-isolated MSOX movie series dataset 20 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [11.4 MGy]

Components

Copper-containing nitrite reductase

Keywords

OXIDOREDUCTASE / electron transfer / Nitrite binding / nitrite reductase

Function / homology

Function and homology information

denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function

Biological species

Bradyrhizobium sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, A.L. / Antonyuk, S.V. / Hasnain, S.S.

Funding support

Argentina,

United Kingdom, 2items

Organization	Grant number	Country
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	PICT 2020-00522	Argentina
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/N013972/1	United Kingdom

Citation

Journal: J.Mol.Biol. / Year: 2024
Title: Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases.
Authors: Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Hasnain, S.S.

History

Deposition	Feb 26, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2024	Group: Database references / Structure summary / Category: citation / citation_author / struct Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.name / _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s68.cif.gz	159.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8s68_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8s68_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8s68_validation.xml.gz	18.7 KB	Display
Data in CIF	8s68_validation.cif.gz	28.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/8s68 ftp://data.pdbj.org/pub/pdb/validation_reports/s6/8s68	HTTPS FTP

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Related structure data

Related structure data	8r8sC 8rflC 8rfoC 8rfpC 8rfqC 8rfrC 8rfsC 8rftC 8rfuC 8rfvC 8rfwC 8rfxC 8rfyC 8rg8C 8rg9C 8rgbC 8rgcC 8rgdC 8ru9C 8rurC 8ryjC 8ryrC 8ryuC 8ryvC 8s0wC 8s2qC 8s5xC 8s5yC 8s63C 8s64C 8s69C 9evmC 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	#186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (2) #254 - Feb 2021 Cellulose Synthase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Copper-containing nitrite reductase

hetero molecules

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

1

A: Copper-containing nitrite reductase

hetero molecules

A: Copper-containing nitrite reductase

hetero molecules

A: Copper-containing nitrite reductase

hetero molecules

defined by author&software
Evidence: gel filtration
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.3, 104.3, 64.8
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-574- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Copper-containing nitrite reductase Mass: 39758.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: ORS375 / Gene: nirK / Plasmid: p22BK / Details (production host): pET-22b(+):blr7089 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)

#1: Protein

Copper-containing nitrite reductase

Mass: 39758.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bradyrhizobium sp. (bacteria) / Strain: ORS375 / Gene: nirK / Plasmid: p22BK / Details (production host): pET-22b(+):blr7089 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)

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Sugars , 2 types, 2 molecules

#4: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#5: Sugar

ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

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Non-polymers , 3 types, 368 molecules

#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.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.52 Å³/Da / Density % sol: 51.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 50 mM Hepes pH 5.5, 1.8 M Ammonium Sulphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.855 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.855 Å / Relative weight: 1
Reflection	Resolution: 1.66→52.204 Å / Num. obs: 47245 / % possible obs: 99.6 % / Redundancy: 4.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.071 / R_rim(I) all: 0.123 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.66→1.69 Å / Redundancy: 4.7 % / R_merge(I) obs: 1.23 / Num. unique obs: 2315 / CC_1/2: 0.316 / R_pim(I) all: 0.876 / R_rim(I) all: 1.523

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
REFMAC	5.8.0425	refinement
xia2		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.66→52.204 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.965 / SU B: 1.992 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.083
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1854	2444	5.176 %
R_work	0.1471	44777	-
all	0.149	-	-
obs	-	47221	99.48 %

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: 26.392 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.282 Å²	-0.141 Å²	0 Å²
2-	-	-0.282 Å²	-0 Å²
3-	-	-	0.913 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→52.204 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2561	0	45	362	2968

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2841
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2718
X-RAY DIFFRACTION	r_angle_refined_deg	1.765	1.839	3899
X-RAY DIFFRACTION	r_angle_other_deg	0.611	1.763	6296
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.458	5	385
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.488	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.567	10	480
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.742	10	118
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	427
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3320
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	614
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	426
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	2397
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1293
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1513
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.2	275
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.168	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.093	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.193	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.16	0.2	106
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.302	0.2	47
X-RAY DIFFRACTION	r_mcbond_it	2.09	2.267	1398
X-RAY DIFFRACTION	r_mcbond_other	2.089	2.269	1399
X-RAY DIFFRACTION	r_mcangle_it	2.909	4.061	1762
X-RAY DIFFRACTION	r_mcangle_other	2.896	4.06	1762
X-RAY DIFFRACTION	r_scbond_it	3.351	2.704	1443
X-RAY DIFFRACTION	r_scbond_other	3.35	2.704	1444
X-RAY DIFFRACTION	r_scangle_it	5.118	4.776	2113
X-RAY DIFFRACTION	r_scangle_other	5.117	4.776	2114
X-RAY DIFFRACTION	r_lrange_it	6.778	29.584	3123
X-RAY DIFFRACTION	r_lrange_other	6.78	29.586	3124

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
1.66-1.703	0.281	191	0.274	3285	0.274	3478	0.945	0.945	99.9425	0.27
1.703-1.75	0.295	152	0.255	3253	0.257	3412	0.945	0.953	99.7948	0.248
1.75-1.8	0.265	180	0.237	3105	0.239	3291	0.956	0.961	99.8177	0.23
1.8-1.856	0.233	154	0.211	3069	0.212	3226	0.963	0.969	99.907	0.196
1.856-1.917	0.204	165	0.19	2955	0.191	3122	0.974	0.975	99.9359	0.174
1.917-1.984	0.213	170	0.184	2841	0.185	3012	0.971	0.977	99.9668	0.165
1.984-2.059	0.205	198	0.167	2701	0.169	2901	0.971	0.982	99.9311	0.149
2.059-2.142	0.158	116	0.145	2684	0.145	2805	0.984	0.987	99.8217	0.13
2.142-2.238	0.176	138	0.146	2550	0.148	2692	0.981	0.987	99.8514	0.128
2.238-2.347	0.174	115	0.132	2459	0.134	2586	0.979	0.989	99.536	0.118
2.347-2.473	0.191	144	0.14	2297	0.143	2446	0.981	0.989	99.7956	0.126
2.473-2.623	0.178	116	0.138	2195	0.14	2318	0.983	0.99	99.698	0.128
2.623-2.803	0.193	129	0.143	2040	0.146	2187	0.98	0.989	99.177	0.137
2.803-3.027	0.187	106	0.141	1881	0.144	2025	0.978	0.988	98.1235	0.141
3.027-3.315	0.171	88	0.13	1775	0.132	1890	0.983	0.989	98.5714	0.133
3.315-3.705	0.149	63	0.121	1605	0.122	1701	0.988	0.991	98.06	0.128
3.705-4.274	0.139	84	0.103	1394	0.105	1509	0.989	0.994	97.9457	0.119
4.274-5.226	0.183	58	0.107	1216	0.11	1285	0.982	0.993	99.144	0.128
5.226-7.354	0.157	48	0.132	943	0.133	1000	0.986	0.989	99.1	0.156
7.354-52.204	0.202	29	0.191	531	0.192	582	0.977	0.976	96.2199	0.241

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