3X1N

Nitrite-bound thermostable copper nitrite reductase at 320 K

PDB DOI: https://doi.org/10.2210/pdb3X1N/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacillus thermodenitrificans NG80-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-11-25 Released: 2015-01-21
Deposition Author(s): Fukuda, Y., Inoue, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.131 (Depositor), 0.140 (DCC)
R-Value Work:
0.115 (Depositor), 0.130 (DCC)
R-Value Observed:
0.115 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

High-temperature and high-resolution crystallography of thermostable copper nitrite reductase.

Fukuda, Y., Inoue, T.

(2015) Chem Commun (Camb) 51: 6532-6535

PubMed: 25563214 Search on PubMed
DOI: https://doi.org/10.1039/c4cc09553g
Primary Citation of Related Structures:
3X1N

PubMed Abstract:
The 1.55 Å resolution thermostable copper nitrite reductase structure at 320 K displayed a near-bidentate binding mode of nitrite distinct from a monodentate mode in a cryogenic structure. To our knowledge, this is the first case in which the difference in substrate binding modes between cryogenic and high-temperature structures has been visualized by crystallography.

Organizational Affiliation

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. y_fukuda@chem.eng.osaka-u.ac.jp.

Macromolecule Content

Total Structure Weight: 38.68 kDa
Atom Count: 2,848
Modelled Residue Count: 298
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite reductase	A	352	Geobacillus thermodenitrificans NG80-2	Mutation(s): 1 Gene Names: nirK EC: 1.7.2.1
UniProt
Find proteins for A4IL26 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IL26 Go to UniProtKB: A4IL26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4IL26
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
NO2 Query on NO2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]