8RVM | pdb_00008rvm

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

PDB DOI: https://doi.org/10.2210/pdb8RVM/pdb

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

Deposited: 2024-02-01 Released: 2024-03-27
Deposition Author(s): Polyakov, K.M., Safoonova, 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: 1.60 Å
R-Value Free:
0.243 (Depositor), 0.196 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)

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 space group P63

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

To be published.

Macromolecule Content

Total Structure Weight: 60.58 kDa
Atom Count: 4,764
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 nitrite c cytochrome c reductase	A [auth YYY]	495	Trichlorobacter ammonificans	Mutation(s): 0

Small Molecules

Ligands 3 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 B [auth YYY] SDF format, chain C [auth YYY] SDF format, chain D [auth YYY] SDF format, chain E [auth YYY] SDF format, chain F [auth YYY] SDF format, chain G [auth YYY] SDF format, chain H [auth YYY] SDF format, chain I [auth YYY] MOL2 format, chain B [auth YYY] MOL2 format, chain C [auth YYY] MOL2 format, chain D [auth YYY] MOL2 format, chain E [auth YYY] MOL2 format, chain F [auth YYY] MOL2 format, chain G [auth YYY] MOL2 format, chain H [auth YYY] MOL2 format, chain I [auth YYY] mmCIF format, chain B [auth YYY] mmCIF format, chain C [auth YYY] mmCIF format, chain D [auth YYY] mmCIF format, chain E [auth YYY] mmCIF format, chain F [auth YYY] mmCIF format, chain G [auth YYY] mmCIF format, chain H [auth YYY] mmCIF format, chain I [auth YYY]	B [auth YYY] C [auth YYY] D [auth YYY] E [auth YYY] F [auth YYY] B [auth YYY], C [auth YYY], D [auth YYY], E [auth YYY], F [auth YYY], G [auth YYY], H [auth YYY], I [auth YYY]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain B [auth YYY] Focus chain C [auth YYY] Focus chain D [auth YYY] Focus chain E [auth YYY] Focus chain F [auth YYY] Focus chain G [auth YYY] Focus chain H [auth YYY] Focus chain I [auth YYY] Interactions & Density Focus chain B [auth YYY] Focus chain C [auth YYY] Focus chain D [auth YYY] Focus chain E [auth YYY] Focus chain F [auth YYY] Focus chain G [auth YYY] Focus chain H [auth YYY] Focus chain I [auth YYY]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth YYY] MOL2 format, chain J [auth YYY] mmCIF format, chain J [auth YYY]	J [auth YYY]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth YYY] Interactions & Density Focus chain J [auth YYY]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth YYY] MOL2 format, chain K [auth YYY] mmCIF format, chain K [auth YYY]	K [auth YYY]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth YYY] Interactions & Density Focus chain K [auth YYY]