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

ID or keywords:

Entry

Database: PDB / ID: 8rvm

Title

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P63

Components

Octaheme nitrite c cytochrome c 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: 1.6 Å

Authors

Polyakov, K.M. / Safoonova, 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 P63
Authors: Polyakov, K.M. / Safoonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.

History

Deposition	Feb 1, 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	8rvm.cif.gz	141.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8rvm.ent.gz		Display	PDB format
PDBx/mmJSON format	8rvm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8rvm_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	8rvm_full_validation.pdf.gz	4.1 MB	Display
Data in XML	8rvm_validation.xml.gz	27.1 KB	Display
Data in CIF	8rvm_validation.cif.gz	40.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rv/8rvm ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rvm	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

YYY: Octaheme nitrite c cytochrome c reductase

hetero molecules

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

1

YYY: Octaheme nitrite c cytochrome c reductase

hetero molecules

YYY: Octaheme nitrite c cytochrome c reductase

hetero molecules

YYY: Octaheme nitrite c cytochrome c reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	114.200, 114.200, 64.800
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	YYY-1077- HOH
2	1	YYY-1120- HOH
3	1	YYY-1151- HOH
4	1	YYY-1183- HOH
5	1	YYY-1189- HOH
6	1	YYY-1191- HOH
7	1	YYY-1198- HOH
8	1	YYY-1203- HOH
9	1	YYY-1204- HOH

#1: Protein	Octaheme nitrite c cytochrome c reductase Mass: 55493.074 Da / Num. of mol.: 1 / 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.: 8 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 505 / 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: 44.04 %
Crystal grow	Temperature: 293 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	Resolution: 1.6→98.9 Å / Num. obs: 59330 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC_1/2: 0.888 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.6→1.74 Å / Num. unique obs: 4437 / CC_1/2: 0.656

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→98.9 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.938 / SU B: 3.034 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.128

	R_factor	Num. reflection	% reflection
R_free	0.2433	2709	5.021 %
R_work	0.1942	51247	-
all	0.197	-	-
obs	-	59330	99.902 %

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: 21.496 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.507 Å²	-0.254 Å²	-0 Å²
2-	-	-0.507 Å²	0 Å²
3-	-	-	1.646 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→98.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3891	0	350	505	4746

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.014	4439
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	3916
X-RAY DIFFRACTION	r_angle_refined_deg	2.794	1.808	6102
X-RAY DIFFRACTION	r_angle_other_deg	1.553	1.674	9108
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.297	5	494
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.6	22.891	211
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.556	15	716
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	11.739	15	1
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.312	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.161	0.2	526
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	4973
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	928
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1070
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	4227
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	2073
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	1937
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	374
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.133	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.095	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.158	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.139	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.173	0.2	43
X-RAY DIFFRACTION	r_mcbond_it	1.849	2.159	1979
X-RAY DIFFRACTION	r_mcbond_other	1.841	2.158	1978
X-RAY DIFFRACTION	r_mcangle_it	2.683	3.234	2472
X-RAY DIFFRACTION	r_mcangle_other	2.683	3.236	2473
X-RAY DIFFRACTION	r_scbond_it	2.079	2.236	2460
X-RAY DIFFRACTION	r_scbond_other	2.077	2.236	2454
X-RAY DIFFRACTION	r_scangle_it	3.137	3.251	3630
X-RAY DIFFRACTION	r_scangle_other	3.134	3.251	3624
X-RAY DIFFRACTION	r_lrange_it	4.675	24.901	5635
X-RAY DIFFRACTION	r_lrange_other	4.597	24.566	5518

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 (%)
1.69-1.734	0.587	165	0.599	3807	X-RAY DIFFRACTION	99.9748
1.734-1.781	0.456	234	0.415	3632	X-RAY DIFFRACTION	99.9225
1.781-1.833	0.347	160	0.284	3578	X-RAY DIFFRACTION	99.7332
1.833-1.889	0.328	198	0.238	3447	X-RAY DIFFRACTION	99.8904
1.889-1.951	0.258	178	0.214	3378	X-RAY DIFFRACTION	99.8876
1.951-2.02	0.253	178	0.221	3278	X-RAY DIFFRACTION	99.9711
2.02-2.096	0.279	164	0.219	3111	X-RAY DIFFRACTION	99.7259
2.096-2.182	0.295	127	0.217	3066	X-RAY DIFFRACTION	99.9687
2.182-2.279	0.25	207	0.2	2850	X-RAY DIFFRACTION	100
2.279-2.39	0.224	149	0.187	2801	X-RAY DIFFRACTION	100
2.39-2.519	0.251	136	0.181	2631	X-RAY DIFFRACTION	99.9639
2.519-2.672	0.238	113	0.177	2545	X-RAY DIFFRACTION	99.9248
2.672-2.856	0.231	146	0.168	2344	X-RAY DIFFRACTION	99.9599
2.856-3.084	0.249	91	0.181	2218	X-RAY DIFFRACTION	99.8702
3.084-3.379	0.239	105	0.182	2013	X-RAY DIFFRACTION	99.9528
3.379-3.777	0.191	91	0.161	1844	X-RAY DIFFRACTION	100
3.777-4.36	0.169	113	0.14	1598	X-RAY DIFFRACTION	99.8832
4.36-5.337	0.169	74	0.142	1374	X-RAY DIFFRACTION	99.931
5.337-7.537	0.282	42	0.157	1093	X-RAY DIFFRACTION	99.8241
7.537-42.878	0.2	38	0.157	611	X-RAY DIFFRACTION	99.084

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