7B04

Structure of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.

PDB DOI: https://doi.org/10.2210/pdb7B04/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candidatus Kuenenia stuttgartiensis
Mutation(s): No

Deposited: 2020-11-18 Released: 2021-07-14
Deposition Author(s): Moreno-Chicano, T., Dietl, A., Akram, M., Barends, T.R.M.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free: 0.255
R-Value Work: 0.223
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex

Chicano, T.M., Dietrich, L., de Almeida, N.M., Akram, M., Hartmann, E., Leidreiter, F., Leopoldus, D., Mueller, M., Sanchez, R., Nuijten, G.H.L., Reimann, J., Seifert, K.A., Schlichting, I., van Niftrik, L., Jetten, M.S.M., Dietl, A., Kartal, B., Parey, K., Barends, T.R.M.

(2021) Nat Microbiol

DOI: https://doi.org/10.1038/s41564-021-00934-8

Macromolecule Content

Total Structure Weight: 1,756.02 kDa
Atom Count: 115,931
Modelled Residue Count: 14,543
Deposited Residue Count: 15,040
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite oxidoreductase subunit B	A, D, G, J, M A, D, G, J, M, P, S, V	410	Candidatus Kuenenia stuttgartiensis	Mutation(s): 0 EC: 1.7.99.4
UniProt
Find proteins for Q1PZD5 (Kuenenia stuttgartiensis) Explore Q1PZD5 Go to UniProtKB: Q1PZD5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1PZD5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite oxidoreductase subunit A	B, E, H, K, N B, E, H, K, N, Q, T, W	1,148	Candidatus Kuenenia stuttgartiensis	Mutation(s): 0 EC: 1.7.99.4
UniProt
Find proteins for Q1PZD8 (Kuenenia stuttgartiensis) Explore Q1PZD8 Go to UniProtKB: Q1PZD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1PZD8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite oxidoreductase subunit C	C, F, I, L, O C, F, I, L, O, R, U, X	322	Candidatus Kuenenia stuttgartiensis	Mutation(s): 0
UniProt
Find proteins for Q1PZD4 (Kuenenia stuttgartiensis) Explore Q1PZD4 Go to UniProtKB: Q1PZD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1PZD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MD1 (Subject of Investigation/LOI) Query on MD1 Download Ideal Coordinates CCD File SDF format, chain BD [auth W] SDF format, chain CA [auth B] SDF format, chain CD [auth W] SDF format, chain DA [auth B] SDF format, chain FC [auth Q] SDF format, chain GC [auth Q] SDF format, chain JB [auth K] SDF format, chain KB [auth K] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain QC [auth T] SDF format, chain RC [auth T] SDF format, chain UB [auth N] SDF format, chain VB [auth N] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain BD [auth W] MOL2 format, chain CA [auth B] MOL2 format, chain CD [auth W] MOL2 format, chain DA [auth B] MOL2 format, chain FC [auth Q] MOL2 format, chain GC [auth Q] MOL2 format, chain JB [auth K] MOL2 format, chain KB [auth K] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain QC [auth T] MOL2 format, chain RC [auth T] MOL2 format, chain UB [auth N] MOL2 format, chain VB [auth N] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H]	BD [auth W] CA [auth B] CD [auth W] DA [auth B] FC [auth Q] BD [auth W], CA [auth B], CD [auth W], DA [auth B], FC [auth Q], GC [auth Q], JB [auth K], KB [auth K], NA [auth E], OA [auth E], QC [auth T], RC [auth T], UB [auth N], VB [auth N], YA [auth H], ZA [auth H]	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ IRGDLSAXQOKWLX-XHEYTWMPSA-N		Interactions Focus chain BD [auth W] Focus chain CA [auth B] Focus chain CD [auth W] Focus chain DA [auth B] Focus chain FC [auth Q] Focus chain GC [auth Q] Focus chain JB [auth K] Focus chain KB [auth K] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QC [auth T] Focus chain RC [auth T] Focus chain UB [auth N] Focus chain VB [auth N] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain BD [auth W] Focus chain CA [auth B] Focus chain CD [auth W] Focus chain DA [auth B] Focus chain FC [auth Q] Focus chain GC [auth Q] Focus chain JB [auth K] Focus chain KB [auth K] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QC [auth T] Focus chain RC [auth T] Focus chain UB [auth N] Focus chain VB [auth N] Focus chain YA [auth H] Focus chain ZA [auth H]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain CB [auth I] SDF format, chain FD [auth X] SDF format, chain GA [auth C] SDF format, chain JC [auth R] SDF format, chain NB [auth L] SDF format, chain RA [auth F] SDF format, chain UC [auth U] SDF format, chain YB [auth O] MOL2 format, chain CB [auth I] MOL2 format, chain FD [auth X] MOL2 format, chain GA [auth C] MOL2 format, chain JC [auth R] MOL2 format, chain NB [auth L] MOL2 format, chain RA [auth F] MOL2 format, chain UC [auth U] MOL2 format, chain YB [auth O]	CB [auth I] FD [auth X] GA [auth C] JC [auth R] NB [auth L] CB [auth I], FD [auth X], GA [auth C], JC [auth R], NB [auth L], RA [auth F], UC [auth U], YB [auth O]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CB [auth I] Focus chain FD [auth X] Focus chain GA [auth C] Focus chain JC [auth R] Focus chain NB [auth L] Focus chain RA [auth F] Focus chain UC [auth U] Focus chain YB [auth O] Interactions & Density Focus chain CB [auth I] Focus chain FD [auth X] Focus chain GA [auth C] Focus chain JC [auth R] Focus chain NB [auth L] Focus chain RA [auth F] Focus chain UC [auth U] Focus chain YB [auth O]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BB [auth H] SDF format, chain BC [auth P] SDF format, chain CC [auth P] SDF format, chain DC [auth P] SDF format, chain ED [auth W] SDF format, chain FA [auth B] SDF format, chain FB [auth J] SDF format, chain GB [auth J] SDF format, chain HB [auth J] SDF format, chain IC [auth Q] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MB [auth K] SDF format, chain MC [auth S] SDF format, chain NC [auth S] SDF format, chain OC [auth S] SDF format, chain QA [auth E] SDF format, chain QB [auth M] SDF format, chain RB [auth M] SDF format, chain SB [auth M] SDF format, chain TC [auth T] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain XB [auth N] SDF format, chain XC [auth V] SDF format, chain Y [auth A] SDF format, chain YC [auth V] SDF format, chain Z [auth A] SDF format, chain ZC [auth V] MOL2 format, chain AA [auth A] MOL2 format, chain BB [auth H] MOL2 format, chain BC [auth P] MOL2 format, chain CC [auth P] MOL2 format, chain DC [auth P] MOL2 format, chain ED [auth W] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth J] MOL2 format, chain GB [auth J] MOL2 format, chain HB [auth J] MOL2 format, chain IC [auth Q] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MB [auth K] MOL2 format, chain MC [auth S] MOL2 format, chain NC [auth S] MOL2 format, chain OC [auth S] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth M] MOL2 format, chain RB [auth M] MOL2 format, chain SB [auth M] MOL2 format, chain TC [auth T] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain XB [auth N] MOL2 format, chain XC [auth V] MOL2 format, chain Y [auth A] MOL2 format, chain YC [auth V] MOL2 format, chain Z [auth A] MOL2 format, chain ZC [auth V]	AA [auth A] BB [auth H] BC [auth P] CC [auth P] DC [auth P] AA [auth A], BB [auth H], BC [auth P], CC [auth P], DC [auth P], ED [auth W], FA [auth B], FB [auth J], GB [auth J], HB [auth J], IC [auth Q], JA [auth D], KA [auth D], LA [auth D], MB [auth K], MC [auth S], NC [auth S], OC [auth S], QA [auth E], QB [auth M], RB [auth M], SB [auth M], TC [auth T], UA [auth G], VA [auth G], WA [auth G], XB [auth N], XC [auth V], Y [auth A], YC [auth V], Z [auth A], ZC [auth V]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BB [auth H] Focus chain BC [auth P] Focus chain CC [auth P] Focus chain DC [auth P] Focus chain ED [auth W] Focus chain FA [auth B] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IC [auth Q] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MB [auth K] Focus chain MC [auth S] Focus chain NC [auth S] Focus chain OC [auth S] Focus chain QA [auth E] Focus chain QB [auth M] Focus chain RB [auth M] Focus chain SB [auth M] Focus chain TC [auth T] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XB [auth N] Focus chain XC [auth V] Focus chain Y [auth A] Focus chain YC [auth V] Focus chain Z [auth A] Focus chain ZC [auth V] Interactions & Density Focus chain AA [auth A] Focus chain BB [auth H] Focus chain BC [auth P] Focus chain CC [auth P] Focus chain DC [auth P] Focus chain ED [auth W] Focus chain FA [auth B] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IC [auth Q] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MB [auth K] Focus chain MC [auth S] Focus chain NC [auth S] Focus chain OC [auth S] Focus chain QA [auth E] Focus chain QB [auth M] Focus chain RB [auth M] Focus chain SB [auth M] Focus chain TC [auth T] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XB [auth N] Focus chain XC [auth V] Focus chain Y [auth A] Focus chain YC [auth V] Focus chain Z [auth A] Focus chain ZC [auth V]
F3S (Subject of Investigation/LOI) Query on F3S Download Ideal Coordinates CCD File SDF format, chain AD [auth V] SDF format, chain BA [auth A] SDF format, chain EC [auth P] SDF format, chain IB [auth J] SDF format, chain MA [auth D] SDF format, chain PC [auth S] SDF format, chain TB [auth M] SDF format, chain XA [auth G] MOL2 format, chain AD [auth V] MOL2 format, chain BA [auth A] MOL2 format, chain EC [auth P] MOL2 format, chain IB [auth J] MOL2 format, chain MA [auth D] MOL2 format, chain PC [auth S] MOL2 format, chain TB [auth M] MOL2 format, chain XA [auth G]	AD [auth V] BA [auth A] EC [auth P] IB [auth J] MA [auth D] AD [auth V], BA [auth A], EC [auth P], IB [auth J], MA [auth D], PC [auth S], TB [auth M], XA [auth G]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain AD [auth V] Focus chain BA [auth A] Focus chain EC [auth P] Focus chain IB [auth J] Focus chain MA [auth D] Focus chain PC [auth S] Focus chain TB [auth M] Focus chain XA [auth G] Interactions & Density Focus chain AD [auth V] Focus chain BA [auth A] Focus chain EC [auth P] Focus chain IB [auth J] Focus chain MA [auth D] Focus chain PC [auth S] Focus chain TB [auth M] Focus chain XA [auth G]
MO (Subject of Investigation/LOI) Query on MO Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain DD [auth W] SDF format, chain EA [auth B] SDF format, chain HC [auth Q] SDF format, chain LB [auth K] SDF format, chain PA [auth E] SDF format, chain SC [auth T] SDF format, chain WB [auth N] MOL2 format, chain AB [auth H] MOL2 format, chain DD [auth W] MOL2 format, chain EA [auth B] MOL2 format, chain HC [auth Q] MOL2 format, chain LB [auth K] MOL2 format, chain PA [auth E] MOL2 format, chain SC [auth T] MOL2 format, chain WB [auth N]	AB [auth H] DD [auth W] EA [auth B] HC [auth Q] LB [auth K] AB [auth H], DD [auth W], EA [auth B], HC [auth Q], LB [auth K], PA [auth E], SC [auth T], WB [auth N]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain DD [auth W] Focus chain EA [auth B] Focus chain HC [auth Q] Focus chain LB [auth K] Focus chain PA [auth E] Focus chain SC [auth T] Focus chain WB [auth N] Interactions & Density Focus chain AB [auth H] Focus chain DD [auth W] Focus chain EA [auth B] Focus chain HC [auth Q] Focus chain LB [auth K] Focus chain PA [auth E] Focus chain SC [auth T] Focus chain WB [auth N]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AC [auth O] SDF format, chain DB [auth I] SDF format, chain EB [auth I] SDF format, chain GD [auth X] SDF format, chain HA [auth C] SDF format, chain HD [auth X] SDF format, chain IA [auth C] SDF format, chain KC [auth R] SDF format, chain LC [auth R] SDF format, chain OB [auth L] SDF format, chain PB [auth L] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain VC [auth U] SDF format, chain WC [auth U] SDF format, chain ZB [auth O] MOL2 format, chain AC [auth O] MOL2 format, chain DB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain GD [auth X] MOL2 format, chain HA [auth C] MOL2 format, chain HD [auth X] MOL2 format, chain IA [auth C] MOL2 format, chain KC [auth R] MOL2 format, chain LC [auth R] MOL2 format, chain OB [auth L] MOL2 format, chain PB [auth L] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain VC [auth U] MOL2 format, chain WC [auth U] MOL2 format, chain ZB [auth O]	AC [auth O] DB [auth I] EB [auth I] GD [auth X] HA [auth C] AC [auth O], DB [auth I], EB [auth I], GD [auth X], HA [auth C], HD [auth X], IA [auth C], KC [auth R], LC [auth R], OB [auth L], PB [auth L], SA [auth F], TA [auth F], VC [auth U], WC [auth U], ZB [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth O] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain GD [auth X] Focus chain HA [auth C] Focus chain HD [auth X] Focus chain IA [auth C] Focus chain KC [auth R] Focus chain LC [auth R] Focus chain OB [auth L] Focus chain PB [auth L] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain VC [auth U] Focus chain WC [auth U] Focus chain ZB [auth O] Interactions & Density Focus chain AC [auth O] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain GD [auth X] Focus chain HA [auth C] Focus chain HD [auth X] Focus chain IA [auth C] Focus chain KC [auth R] Focus chain LC [auth R] Focus chain OB [auth L] Focus chain PB [auth L] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain VC [auth U] Focus chain WC [auth U] Focus chain ZB [auth O]