5ZL1 | pdb_00005zl1

Hexameric structure of copper-containing nitrite reductase of an anammox organism KSU-1

PDB DOI: https://doi.org/10.2210/pdb5ZL1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candidatus Jettenia caeni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-26 Released: 2019-04-10
Deposition Author(s): Hira, D., Matsumura, M., Kitamura, R., Fujii, T.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.254 (Depositor), 0.240 (DCC)
R-Value Work:
0.240 (Depositor), 0.230 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Hexameric structure of copper-containing nitrite reductase of an anammox organism KSU-1

Hira, D., Matsumura, M., Kitamura, R., Fujii, T.

To be published.

Macromolecule Content

Total Structure Weight: 145.02 kDa
Atom Count: 9,615
Modeled Residue Count: 1,224
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative copper-type nitrite reductase	A, B, C, D	326	Candidatus Jettenia caeni	Mutation(s): 0 Gene Names: KSU1_D0929 EC: 1.7.2.1
UniProt
Find proteins for I3IR93 (Candidatus Jettenia caeni) Explore I3IR93 Go to UniProtKB: I3IR93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3IR93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], Q [auth C], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], P [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.254 (Depositor), 0.240 (DCC)
R-Value Work: 0.240 (Depositor), 0.230 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 270.217	α = 90
b = 270.217	β = 90
c = 128.909	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JSPS KAKENHI 16K07703

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary