PDB-8rxu: Crystal structure of octaheme nitrite reductase from Trichlorobac...

ID or keywords:

Entry

Database: PDB / ID: 8rxu

Title

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P21

Components

Octaheme nitrite reductase

Keywords

OXIDOREDUCTASE / octaheme nitrite reductase / wild type

Function / homology

HEME C / PHOSPHATE ION

Function and homology information

Biological species

Trichlorobacter ammonificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.737 Å

Authors

Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.

Funding support

Russian Federation, 1items

Citation

Journal: To Be Published
Title: Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P21
Authors: Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.

History

Deposition	Feb 8, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rxu.cif.gz	360.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8rxu.ent.gz		Display	PDB format
PDBx/mmJSON format	8rxu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rx/8rxu ftp://data.pdbj.org/pub/pdb/validation_reports/rx/8rxu	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&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 (1) #111 - Mar 2009 Hydrogenase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

AAA: Octaheme nitrite reductase

MMM: Octaheme nitrite reductase

YYY: Octaheme nitrite reductase

hetero molecules

182 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	114.200, 64.800, 114.200
Angle α, β, γ (deg.)	90.000, 119.900, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Octaheme nitrite reductase Mass: 55493.074 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trichlorobacter ammonificans (bacteria)
#2: Chemical	... ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.2 Å³/Da / Density % sol: 44.12 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 17-20 % PEG 3350, 0.1 M Bis-Tris

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97242 Å

Detector

Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 19, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97242 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.4003
pseudo-merohedral	2	2	L, K, -H-L	2	0.2901
pseudo-merohedral	3	3	-H-L, K, H	3	0.3097

Reflection

Resolution: 1.737→42.877 Å / Num. obs: 145919 / % possible obs: 98 % / Redundancy: 4.2 % / CC_1/2: 0.996 / Net I/σ(I): 10.7

Reflection shell

Resolution: 1.737→1.83 Å / R_merge(I) obs: 0.956 / Num. unique obs: 101804 / CC_1/2: 0.844

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.737→42.877 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.929 / SU B: 2.262 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2542	7348	5.036 %
R_work	0.1913	138571	-
all	0.195	-	-
obs	-	145919	97.76 %

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: 21.354 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.737 Å²	-0 Å²	5.607 Å²
2-	-	9.76 Å²	0 Å²
3-	-	-	-7.023 Å²

Refinement step

Cycle: LAST / Resolution: 1.737→42.877 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11665	0	1050	950	13665

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.014	13281
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	11720
X-RAY DIFFRACTION	r_angle_refined_deg	3.056	1.808	18260
X-RAY DIFFRACTION	r_angle_other_deg	1.445	1.675	27242
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.494	5	1484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.525	22.812	626
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.199	15	2127
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	12.447	15	3
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.883	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.172	0.2	1572
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	14902
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	2785
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	3838
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	13696
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	5918
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.096	0.2	6027
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	855
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.098	0.2	15
X-RAY DIFFRACTION	r_metal_ion_refined	0.126	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.198	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.181	2.275	5939
X-RAY DIFFRACTION	r_mcbond_other	2.181	2.275	5938
X-RAY DIFFRACTION	r_mcangle_it	2.893	3.412	7419
X-RAY DIFFRACTION	r_mcangle_other	2.893	3.412	7420
X-RAY DIFFRACTION	r_scbond_it	1.97	2.277	7342
X-RAY DIFFRACTION	r_scbond_other	1.969	2.277	7328
X-RAY DIFFRACTION	r_scangle_it	2.603	3.375	10840
X-RAY DIFFRACTION	r_scangle_other	2.601	3.375	10822
X-RAY DIFFRACTION	r_lrange_it	3.976	26.056	17009
X-RAY DIFFRACTION	r_lrange_other	3.951	26.027	16896

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.737-1.782	0.601	612	0.473	9410	X-RAY DIFFRACTION	91.2501
1.782-1.831	0.45	479	0.315	9715	X-RAY DIFFRACTION	95.6106
1.831-1.884	0.377	491	0.271	9809	X-RAY DIFFRACTION	99.1242
1.884-1.942	0.315	463	0.224	9608	X-RAY DIFFRACTION	98.9973
1.942-2.006	0.309	415	0.229	9291	X-RAY DIFFRACTION	99.0105
2.006-2.076	0.285	444	0.221	8856	X-RAY DIFFRACTION	97.9463
2.076-2.155	0.283	449	0.212	8569	X-RAY DIFFRACTION	98.1498
2.155-2.243	0.283	466	0.204	8116	X-RAY DIFFRACTION	97.756
2.243-2.342	0.26	452	0.185	7754	X-RAY DIFFRACTION	96.7346
2.342-2.457	0.244	470	0.184	7556	X-RAY DIFFRACTION	99.7142
2.457-2.589	0.247	320	0.183	7409	X-RAY DIFFRACTION	99.6647
2.589-2.746	0.248	344	0.186	6923	X-RAY DIFFRACTION	99.5616
2.746-2.936	0.277	340	0.187	6449	X-RAY DIFFRACTION	98.4627
2.936-3.171	0.232	361	0.189	5811	X-RAY DIFFRACTION	97.4885
3.171-3.473	0.264	288	0.19	5462	X-RAY DIFFRACTION	96.428
3.473-3.882	0.188	344	0.159	4955	X-RAY DIFFRACTION	99.8681
3.882-4.482	0.185	187	0.129	4524	X-RAY DIFFRACTION	99.7882
4.482-5.486	0.181	212	0.144	3825	X-RAY DIFFRACTION	99.5316
5.486-7.747	0.189	157	0.164	2813	X-RAY DIFFRACTION	94.7368
7.747-42.877	0.204	54	0.158	1716	X-RAY DIFFRACTION	98.5523

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