8RXU | pdb_00008rxu

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

PDB DOI: https://doi.org/10.2210/pdb8RXU/pdb

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

Deposited: 2024-02-08 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: 1.74 Å
R-Value Free:
0.254 (Depositor), 0.261 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (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 P21

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: 181.73 kDa
Atom Count: 13,690
Modeled Residue Count: 1,485
Deposited Residue Count: 1,485
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaheme nitrite reductase	A [auth AAA], B [auth MMM], C [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 Z [auth YYY] SDF format, chain Y [auth YYY] SDF format, chain X [auth YYY] SDF format, chain U [auth MMM] SDF format, chain T [auth MMM] SDF format, chain S [auth MMM] SDF format, chain R [auth MMM] SDF format, chain Q [auth MMM] SDF format, chain P [auth MMM] SDF format, chain O [auth MMM] SDF format, chain N [auth MMM] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain EA [auth YYY] SDF format, chain E [auth AAA] SDF format, chain DA [auth YYY] SDF format, chain D [auth AAA] SDF format, chain CA [auth YYY] SDF format, chain BA [auth YYY] SDF format, chain AA [auth YYY] MOL2 format, chain Z [auth YYY] MOL2 format, chain Y [auth YYY] MOL2 format, chain X [auth YYY] MOL2 format, chain U [auth MMM] MOL2 format, chain T [auth MMM] MOL2 format, chain S [auth MMM] MOL2 format, chain R [auth MMM] MOL2 format, chain Q [auth MMM] MOL2 format, chain P [auth MMM] MOL2 format, chain O [auth MMM] MOL2 format, chain N [auth MMM] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain EA [auth YYY] MOL2 format, chain E [auth AAA] MOL2 format, chain DA [auth YYY] MOL2 format, chain D [auth AAA] MOL2 format, chain CA [auth YYY] MOL2 format, chain BA [auth YYY] MOL2 format, chain AA [auth YYY] mmCIF format, chain Z [auth YYY] mmCIF format, chain Y [auth YYY] mmCIF format, chain X [auth YYY] mmCIF format, chain U [auth MMM] mmCIF format, chain T [auth MMM] mmCIF format, chain S [auth MMM] mmCIF format, chain R [auth MMM] mmCIF format, chain Q [auth MMM] mmCIF format, chain P [auth MMM] mmCIF format, chain O [auth MMM] mmCIF format, chain N [auth MMM] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain EA [auth YYY] mmCIF format, chain E [auth AAA] mmCIF format, chain DA [auth YYY] mmCIF format, chain D [auth AAA] mmCIF format, chain CA [auth YYY] mmCIF format, chain BA [auth YYY] mmCIF format, chain AA [auth YYY]	AA [auth YYY] BA [auth YYY] CA [auth YYY] D [auth AAA] DA [auth YYY] AA [auth YYY], BA [auth YYY], CA [auth YYY], D [auth AAA], DA [auth YYY], E [auth AAA], EA [auth YYY], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], N [auth MMM], O [auth MMM], P [auth MMM], Q [auth MMM], R [auth MMM], S [auth MMM], T [auth MMM], U [auth MMM], X [auth YYY], Y [auth YYY], Z [auth YYY]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain AA [auth YYY] Focus chain BA [auth YYY] Focus chain CA [auth YYY] Focus chain D [auth AAA] Focus chain DA [auth YYY] Focus chain E [auth AAA] Focus chain EA [auth YYY] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain N [auth MMM] Focus chain O [auth MMM] Focus chain P [auth MMM] Focus chain Q [auth MMM] Focus chain R [auth MMM] Focus chain S [auth MMM] Focus chain T [auth MMM] Focus chain U [auth MMM] Focus chain X [auth YYY] Focus chain Y [auth YYY] Focus chain Z [auth YYY] Interactions & Density Focus chain AA [auth YYY] Focus chain BA [auth YYY] Focus chain CA [auth YYY] Focus chain D [auth AAA] Focus chain DA [auth YYY] Focus chain E [auth AAA] Focus chain EA [auth YYY] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain N [auth MMM] Focus chain O [auth MMM] Focus chain P [auth MMM] Focus chain Q [auth MMM] Focus chain R [auth MMM] Focus chain S [auth MMM] Focus chain T [auth MMM] Focus chain U [auth MMM] Focus chain X [auth YYY] Focus chain Y [auth YYY] Focus chain Z [auth YYY]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth MMM] SDF format, chain M [auth AAA] SDF format, chain GA [auth YYY] MOL2 format, chain W [auth MMM] MOL2 format, chain M [auth AAA] MOL2 format, chain GA [auth YYY] mmCIF format, chain W [auth MMM] mmCIF format, chain M [auth AAA] mmCIF format, chain GA [auth YYY]	GA [auth YYY], M [auth AAA], W [auth MMM]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth YYY] Focus chain M [auth AAA] Focus chain W [auth MMM] Interactions & Density Focus chain GA [auth YYY] Focus chain M [auth AAA] Focus chain W [auth MMM]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain V [auth MMM] SDF format, chain L [auth AAA] SDF format, chain FA [auth YYY] MOL2 format, chain V [auth MMM] MOL2 format, chain L [auth AAA] MOL2 format, chain FA [auth YYY] mmCIF format, chain V [auth MMM] mmCIF format, chain L [auth AAA] mmCIF format, chain FA [auth YYY]	FA [auth YYY], L [auth AAA], V [auth MMM]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain FA [auth YYY] Focus chain L [auth AAA] Focus chain V [auth MMM] Interactions & Density Focus chain FA [auth YYY] Focus chain L [auth AAA] Focus chain V [auth MMM]