8RV0 | pdb_00008rv0

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite

PDB DOI: https://doi.org/10.2210/pdb8RV0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trichlorobacter ammonificans
Mutation(s): No

Deposited: 2024-01-31 Released: 2024-03-27
Deposition Author(s): Polyakov, K.M., Safonova, T.N., Osipov, E., Popov, A.N., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.255 (Depositor), 0.254 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite

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

To be published.

Macromolecule Content

Total Structure Weight: 60.56 kDa
Atom Count: 4,709
Modeled Residue Count: 495
Deposited Residue Count: 495
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaheme cytochrome c nitrite reductase	A [auth Y]	495	Trichlorobacter ammonificans	Mutation(s): 0 EC: 1.7.2.2
UniProt
Find proteins for A0AAN0NP99 (Trichlorobacter ammonificans) Explore A0AAN0NP99 Go to UniProtKB: A0AAN0NP99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAN0NP99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain I [auth Y] SDF format, chain H [auth Y] SDF format, chain G [auth Y] SDF format, chain F [auth Y] SDF format, chain E [auth Y] SDF format, chain D [auth Y] SDF format, chain C [auth Y] SDF format, chain B [auth Y] MOL2 format, chain I [auth Y] MOL2 format, chain H [auth Y] MOL2 format, chain G [auth Y] MOL2 format, chain F [auth Y] MOL2 format, chain E [auth Y] MOL2 format, chain D [auth Y] MOL2 format, chain C [auth Y] MOL2 format, chain B [auth Y] mmCIF format, chain I [auth Y] mmCIF format, chain H [auth Y] mmCIF format, chain G [auth Y] mmCIF format, chain F [auth Y] mmCIF format, chain E [auth Y] mmCIF format, chain D [auth Y] mmCIF format, chain C [auth Y] mmCIF format, chain B [auth Y]	B [auth Y] C [auth Y] D [auth Y] E [auth Y] F [auth Y] B [auth Y], C [auth Y], D [auth Y], E [auth Y], F [auth Y], G [auth Y], H [auth Y], I [auth Y]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain B [auth Y] Focus chain C [auth Y] Focus chain D [auth Y] Focus chain E [auth Y] Focus chain F [auth Y] Focus chain G [auth Y] Focus chain H [auth Y] Focus chain I [auth Y] Interactions & Density Focus chain B [auth Y] Focus chain C [auth Y] Focus chain D [auth Y] Focus chain E [auth Y] Focus chain F [auth Y] Focus chain G [auth Y] Focus chain H [auth Y] Focus chain I [auth Y]
NO2 (Subject of Investigation/LOI) Query on NO2 Download:Ideal Coordinates CCD File SDF format, chain K [auth Y] MOL2 format, chain K [auth Y] mmCIF format, chain K [auth Y]	K [auth Y]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain K [auth Y] Interactions & Density Focus chain K [auth Y]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth Y] MOL2 format, chain L [auth Y] mmCIF format, chain L [auth Y]	L [auth Y]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth Y] Interactions & Density Focus chain L [auth Y]
NO (Subject of Investigation/LOI) Query on NO Download:Ideal Coordinates CCD File SDF format, chain J [auth Y] MOL2 format, chain J [auth Y] mmCIF format, chain J [auth Y]	J [auth Y]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain J [auth Y] Interactions & Density Focus chain J [auth Y]