6L46

High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.112 
  • R-Value Work: 0.097 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase

Fukuda, Y.Hirano, Y.Kusaka, K.Inoue, T.Tamada, T.

(2020) Proc.Natl.Acad.Sci.USA --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-containing nitrite reductase
A
323Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for A0A1W6VP04 (Geobacillus thermodenitrificans)
Go to UniProtKB:  A0A1W6VP04
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
DOD
Query on DOD

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A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 114.212α = 90.00
b = 114.212β = 90.00
c = 83.688γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
STARGazerdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release