PDB-8s5y: MSOX movie series dataset 40 (22.8 MGy) for as isolated BrJNiR (C...

ID or keywords:

Entry

Database: PDB / ID: 8s5y

Title

MSOX movie series dataset 40 (22.8 MGy) for as isolated BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110) at pH 8.

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: 1.3 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. / Martin Ferroni, F. / Horrell, S. / Dante Brondino, C. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Samar Hasnain, S.

History

Deposition	Feb 26, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s5y.cif.gz	372.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8s5y.ent.gz	249.1 KB	Display	PDB format
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Validation report

Summary document	8s5y_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8s5y_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8s5y_validation.xml.gz	20.1 KB	Display
Data in CIF	8s5y_validation.cif.gz	31.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/8s5y ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s5y	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 8ryjC 8ryrC 8ryuC 8ryvC 8s0wC 8s2qC 8s5xC 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	#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

40.8 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)	104.26, 104.26, 64.66
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	173
Space group name H-M	P6₃

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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 Q89EJ6 / 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 Q89EJ6 / Production host:

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

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Sugars , 2 types, 2 molecules

#3: 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

#4: 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, 480 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
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 472 / 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: 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: 0.775 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: 0.775 Å / Relative weight: 1
Reflection	Resolution: 1.3→64.66 Å / Num. obs: 98197 / % possible obs: 100 % / Redundancy: 9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.163 / R_pim(I) all: 0.084 / R_rim(I) all: 0.184 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.3→1.32 Å / Redundancy: 7.6 % / R_merge(I) obs: 1.791 / Num. unique obs: 4872 / CC_1/2: 0.41 / R_pim(I) all: 0.969 / R_rim(I) all: 2.049

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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: 1.3→45.187 Å / Cor.coef. F_o:F_c: 0.987 / Cor.coef. F_o:F_c free: 0.983 / SU B: 1.709 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.036
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1434	5049	5.143 %
R_work	0.1177	93120	-
all	0.119	-	-
obs	-	98169	99.973 %

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: 19.224 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.018 Å²	0.009 Å²	0 Å²
2-	-	0.018 Å²	0 Å²
3-	-	-	-0.059 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→45.187 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2551	0	55	472	3078

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2902
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2775
X-RAY DIFFRACTION	r_angle_refined_deg	1.834	1.846	3985
X-RAY DIFFRACTION	r_angle_other_deg	0.611	1.762	6438
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.508	5	398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.704	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.389	10	511
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.216	10	116
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	438
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3364
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	606
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	438
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	2396
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1315
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1543
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.222	0.2	334
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.165	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.124	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	58
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.016	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	4.546	1.544	1418
X-RAY DIFFRACTION	r_mcbond_other	4.529	1.543	1418
X-RAY DIFFRACTION	r_mcangle_it	6.378	2.78	1791
X-RAY DIFFRACTION	r_mcangle_other	6.393	2.783	1792
X-RAY DIFFRACTION	r_scbond_it	6.609	1.901	1484
X-RAY DIFFRACTION	r_scbond_other	6.321	1.859	1461
X-RAY DIFFRACTION	r_scangle_it	9.493	3.352	2164
X-RAY DIFFRACTION	r_scangle_other	9.167	3.272	2129
X-RAY DIFFRACTION	r_lrange_it	17.514	24.571	3262
X-RAY DIFFRACTION	r_lrange_other	13.827	18.355	3074
X-RAY DIFFRACTION	r_rigid_bond_restr	3.678	3	5677

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
1.3-1.334	0.259	425	0.265	6806	0.265	7231	0.953	0.949	100	0.262
1.334-1.37	0.269	401	0.236	6662	0.238	7063	0.948	0.961	100	0.23
1.37-1.41	0.241	361	0.214	6512	0.216	6873	0.96	0.968	100	0.204
1.41-1.453	0.227	313	0.192	6313	0.194	6626	0.963	0.974	100	0.177
1.453-1.501	0.201	298	0.161	6160	0.163	6458	0.972	0.983	100	0.142
1.501-1.554	0.17	311	0.138	5934	0.14	6245	0.983	0.988	100	0.116
1.554-1.612	0.148	293	0.124	5752	0.125	6045	0.987	0.99	100	0.1
1.612-1.678	0.17	272	0.123	5514	0.125	5786	0.982	0.989	100	0.094
1.678-1.752	0.152	309	0.111	5253	0.113	5562	0.984	0.991	100	0.083
1.752-1.838	0.143	269	0.111	5054	0.112	5327	0.986	0.991	99.9249	0.081
1.838-1.937	0.139	295	0.109	4765	0.111	5062	0.987	0.992	99.9605	0.079
1.937-2.054	0.126	244	0.098	4548	0.1	4796	0.99	0.994	99.9166	0.081
2.054-2.196	0.122	243	0.085	4278	0.087	4524	0.991	0.995	99.9337	0.074
2.196-2.371	0.107	241	0.08	3970	0.081	4214	0.993	0.996	99.9288	0.073
2.371-2.597	0.11	172	0.092	3703	0.093	3881	0.992	0.995	99.8454	0.091
2.597-2.902	0.141	180	0.101	3334	0.103	3516	0.99	0.995	99.9431	0.105
2.902-3.349	0.12	131	0.1	2975	0.101	3106	0.992	0.994	100	0.111
3.349-4.096	0.115	143	0.096	2497	0.097	2640	0.992	0.995	100	0.112
4.096-5.769	0.112	94	0.098	1962	0.099	2056	0.993	0.994	100	0.124
5.769-45.187	0.17	54	0.18	1128	0.18	1182	0.983	0.977	100	0.221

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