PDB-9fuk: CRYSTAL STRUCTURE OF NITRIC OXIDE-TREATED Q262N MUTANT OF THREE-D...

ID or keywords:

Entry

Database: PDB / ID: 9fuk

Title

CRYSTAL STRUCTURE OF NITRIC OXIDE-TREATED Q262N MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

Components

Copper-containing nitrite reductase

Keywords

OXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN

Function / homology

Function and homology information

nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function

Biological species

Ralstonia pickettii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.09 Å

Authors

Petchyam, N. / Antonyuk, S. / Hasnain, S.S.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.

History

Deposition	Jun 26, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fuk.cif.gz	507.5 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	9fuk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9fuk_validation.pdf.gz	799.9 KB	Display	wwPDB validaton report
Full document	9fuk_full_validation.pdf.gz	803 KB	Display
Data in XML	9fuk_validation.xml.gz	32.6 KB	Display
Data in CIF	9fuk_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fu/9fuk ftp://data.pdbj.org/pub/pdb/validation_reports/fu/9fuk	HTTPS FTP

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Related structure data

Related structure data	7qq2C 8qgfC 9fuhC 9fuiC 3ziy 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	#36 - Dec 2002 Cytochrome c similarity (4) #111 - Mar 2009 Hydrogenase similarity (4) #177 - Sep 2014 Apoptosomes similarity (4) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (4) #137 - May 2011 Cytochrome bc1 similarity (3) #59 - Nov 2004 Photosystem II similarity (3)

Deposited unit

A: Copper-containing nitrite reductase

hetero molecules

49.5 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
Evidence: gel filtration
148 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.069, 128.069, 86.352
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-197- ARG
2	1	A-1314- HOH
3	1	A-1318- HOH
4	1	A-1379- HOH
5	1	A-1382- HOH
6	1	A-1393- HOH
7	1	A-1415- HOH

#1: Protein	Copper-containing nitrite reductase Mass: 48731.145 Da / Num. of mol.: 1 / Mutation: Q262N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: Rpic_4015 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UHR8, nitrite reductase (NO-forming)
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.8 Å³/Da / Density % sol: 56.02 % / Description: Brown red crystal
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.09→37.74 Å / Num. obs: 216270 / % possible obs: 87.2 % / Redundancy: 2.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_pim(I) all: 0.03 / R_rim(I) all: 0.055 / Χ²: 0.9 / Net I/σ(I): 9.2
Reflection shell	Resolution: 1.14→1.16 Å / % possible obs: 82.9 % / Redundancy: 1.9 % / R_merge(I) obs: 0.907 / Num. measured all: 14739 / Num. unique obs: 7916 / CC_1/2: 0.374 / R_pim(I) all: 0.684 / R_rim(I) all: 1.143 / Χ²: 0.92 / Net I/σ(I) obs: 0.9

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.09→37.74 Å / Cor.coef. F_o:F_c: 0.989 / Cor.coef. F_o:F_c free: 0.986 / WR_factor R_free: 0.116 / WR_factor R_work: 0.099 / SU B: 0.763 / SU ML: 0.015 / Average fsc free: 0.9841 / Average fsc work: 0.9861 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1223	10975	5.075 %	RANDOM
R_work	0.1066	205295	-	-
all	0.107	-	-	-
obs	-	216270	98.146 %	-

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: 15.283 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.127 Å²	-0.063 Å²	0 Å²
2-	-	-0.127 Å²	0 Å²
3-	-	-	0.412 Å²

Refinement step

Cycle: LAST / Resolution: 1.09→37.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3428	0	45	821	4294

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	4050
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3863
X-RAY DIFFRACTION	r_angle_refined_deg	1.775	1.847	5608
X-RAY DIFFRACTION	r_angle_other_deg	0.632	1.762	8999
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.063	5	580
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.715	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.149	10	678
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.835	10	175
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	609
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4939
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	929
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	747
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	3376
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1907
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2011
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	635
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.087	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.133	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.248	0.2	37
X-RAY DIFFRACTION	r_nbd_other	0.233	0.2	173
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.251	0.2	81
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.073	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.095	1.208	1994
X-RAY DIFFRACTION	r_mcbond_other	3.069	1.208	1994
X-RAY DIFFRACTION	r_mcangle_it	4.531	2.184	2534
X-RAY DIFFRACTION	r_mcangle_other	4.54	2.186	2535
X-RAY DIFFRACTION	r_scbond_it	4.348	1.388	2056
X-RAY DIFFRACTION	r_scbond_other	4.349	1.389	2054
X-RAY DIFFRACTION	r_scangle_it	6.345	2.471	3016
X-RAY DIFFRACTION	r_scangle_other	6.345	2.47	3016
X-RAY DIFFRACTION	r_lrange_it	17.705	20.624	4993
X-RAY DIFFRACTION	r_lrange_other	12.457	15.447	4602
X-RAY DIFFRACTION	r_rigid_bond_restr	2.967	3	7913

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
1.09-1.119	0.286	684	0.29	12581	0.29	16334	0.937	0.94	81.211	0.288
1.119-1.149	0.253	721	0.25	14322	0.25	15908	0.957	0.959	94.5625	0.24
1.149-1.182	0.213	810	0.207	14532	0.207	15370	0.973	0.974	99.8178	0.189
1.182-1.219	0.19	690	0.178	14362	0.178	15056	0.98	0.982	99.9734	0.156
1.219-1.259	0.171	708	0.157	13807	0.158	14524	0.984	0.986	99.938	0.136
1.259-1.303	0.158	766	0.138	13241	0.14	14017	0.986	0.989	99.9287	0.118
1.303-1.352	0.126	642	0.12	12893	0.12	13543	0.991	0.991	99.9409	0.1
1.352-1.407	0.115	665	0.099	12392	0.1	13058	0.992	0.994	99.9923	0.083
1.407-1.47	0.104	669	0.089	11876	0.09	12548	0.993	0.995	99.9761	0.074
1.47-1.541	0.099	592	0.076	11354	0.077	11946	0.994	0.997	100	0.065
1.541-1.624	0.091	610	0.07	10774	0.071	11385	0.995	0.997	99.9912	0.062
1.624-1.723	0.087	530	0.069	10239	0.07	10769	0.995	0.997	100	0.063
1.723-1.841	0.093	510	0.073	9598	0.074	10109	0.995	0.997	99.9901	0.069
1.841-1.989	0.092	435	0.078	8989	0.079	9424	0.996	0.997	100	0.076
1.989-2.178	0.097	487	0.085	8154	0.085	8641	0.995	0.997	100	0.085
2.178-2.434	0.105	427	0.082	7398	0.083	7825	0.993	0.996	100	0.086
2.434-2.808	0.103	329	0.088	6597	0.089	6926	0.994	0.995	100	0.096
2.808-3.435	0.112	296	0.097	5555	0.098	5851	0.992	0.994	100	0.113
3.435-4.838	0.119	223	0.103	4300	0.104	4523	0.994	0.995	100	0.124
4.838-37.74	0.178	181	0.176	2331	0.176	2518	0.986	0.988	99.7617	0.207

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