PDB-8ryu: High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the c...

ID or keywords:

Entry

Database: PDB / ID: 8ryu

Title

High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [6.9 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: 1.45 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 9, 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	8ryu.cif.gz	164.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8ryu_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8ryu_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8ryu_validation.xml.gz	19.3 KB	Display
Data in CIF	8ryu_validation.cif.gz	30.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ry/8ryu ftp://data.pdbj.org/pub/pdb/validation_reports/ry/8ryu	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 8ryvC 8s0wC 8s2qC 8s5xC 8s5yC 8s63C 8s64C 8s68C 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	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #41 - May 2003 Hemoglobin similarity (1)

Deposited unit

A: Copper-containing nitrite reductase

hetero molecules

40.8 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, 64.47
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-772- HOH

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Protein / Sugars , 2 types, 2 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)

#2: Polysaccharide

beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 428 molecules

#3: 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
#4: Chemical	ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-NO2 / NITRITE ION Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₂
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.55 Å³/Da / Density % sol: 51.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris pH 7.3, 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: 0.77491 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.77491 Å / Relative weight: 1
Reflection	Resolution: 1.45→45.204 Å / Num. obs: 70743 / % possible obs: 100 % / Redundancy: 5.5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.058 / R_rim(I) all: 0.101 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.45→1.47 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.999 / Num. unique obs: 3508 / CC_1/2: 0.392 / R_pim(I) all: 0.785 / R_rim(I) all: 1.281

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→45.204 Å / Cor.coef. F_o:F_c: 0.982 / Cor.coef. F_o:F_c free: 0.974 / SU B: 1.134 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.053
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1643	3653	5.165 %
R_work	0.1403	67069	-
all	0.142	-	-
obs	-	70722	99.96 %

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: 20.598 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.087 Å²	-0.043 Å²	0 Å²
2-	-	-0.087 Å²	-0 Å²
3-	-	-	0.281 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→45.204 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2562	0	55	419	3036

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2878
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2744
X-RAY DIFFRACTION	r_angle_refined_deg	1.932	1.838	3946
X-RAY DIFFRACTION	r_angle_other_deg	0.637	1.758	6364
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.723	5	388
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.64	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.74	10	490
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.776	10	117
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	434
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3346
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	604
X-RAY DIFFRACTION	r_nbd_refined	0.257	0.2	440
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	2371
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1290
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1489
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	310
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.048	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.127	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.147	0.2	115
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.243	0.2	50
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.018	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.844	1.752	1417
X-RAY DIFFRACTION	r_mcbond_other	1.836	1.751	1416
X-RAY DIFFRACTION	r_mcangle_it	2.659	3.14	1785
X-RAY DIFFRACTION	r_mcangle_other	2.661	3.142	1786
X-RAY DIFFRACTION	r_scbond_it	2.817	2.086	1461
X-RAY DIFFRACTION	r_scbond_other	2.816	2.086	1462
X-RAY DIFFRACTION	r_scangle_it	4.13	3.681	2138
X-RAY DIFFRACTION	r_scangle_other	4.129	3.681	2139
X-RAY DIFFRACTION	r_lrange_it	5.901	24.026	3197
X-RAY DIFFRACTION	r_lrange_other	5.903	24.026	3197

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
1.45-1.488	0.288	261	0.278	4936	0.279	5199	0.937	0.944	99.9615	0.278
1.488-1.528	0.269	257	0.253	4828	0.254	5086	0.949	0.955	99.9803	0.25
1.528-1.573	0.238	222	0.231	4732	0.231	4954	0.961	0.963	100	0.225
1.573-1.621	0.241	269	0.21	4494	0.212	4763	0.959	0.97	100	0.201
1.621-1.674	0.207	214	0.197	4454	0.197	4668	0.972	0.974	100	0.184
1.674-1.733	0.198	276	0.171	4205	0.173	4481	0.974	0.981	100	0.157
1.733-1.798	0.169	241	0.161	4110	0.162	4351	0.983	0.983	100	0.145
1.798-1.871	0.177	229	0.143	3932	0.145	4163	0.982	0.987	99.952	0.126
1.871-1.954	0.172	221	0.137	3807	0.139	4029	0.98	0.988	99.9752	0.124
1.954-2.05	0.151	149	0.131	3679	0.132	3828	0.986	0.989	100	0.12
2.05-2.16	0.15	188	0.121	3471	0.123	3659	0.986	0.991	100	0.114
2.16-2.291	0.158	165	0.12	3286	0.122	3451	0.985	0.991	100	0.115
2.291-2.449	0.164	161	0.117	3079	0.119	3241	0.985	0.992	99.9691	0.115
2.449-2.644	0.156	168	0.122	2873	0.124	3043	0.987	0.992	99.9343	0.122
2.644-2.896	0.15	148	0.126	2654	0.128	2802	0.986	0.991	100	0.131
2.896-3.236	0.148	126	0.126	2406	0.127	2537	0.987	0.991	99.8029	0.138
3.236-3.733	0.114	104	0.114	2133	0.114	2239	0.993	0.993	99.9107	0.127
3.733-4.564	0.143	137	0.107	1772	0.109	1914	0.989	0.994	99.7388	0.13
4.564-6.422	0.12	66	0.115	1415	0.116	1484	0.991	0.992	99.7978	0.146
6.422-45.204	0.213	51	0.184	803	0.185	855	0.967	0.978	99.883	0.235

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