4O65

Crystal structure of the cupredoxin domain of amoB from Nitrosocaldus yellowstonii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.796 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily.

Lawton, T.J.Ham, J.Sun, T.Rosenzweig, A.C.

(2014) Proteins 82: 2263-2267

  • DOI: 10.1002/prot.24535

  • PubMed Abstract: 
  • The ammonia monooxygenase (AMO)/particulate methane monooxygenase (pMMO) superfamily is a diverse group of membrane-bound enzymes of which only pMMO has been characterized on the molecular level. The pMMO active site is believed to reside in the solu ...

    The ammonia monooxygenase (AMO)/particulate methane monooxygenase (pMMO) superfamily is a diverse group of membrane-bound enzymes of which only pMMO has been characterized on the molecular level. The pMMO active site is believed to reside in the soluble N-terminal region of the pmoB subunit. To understand the degree of structural conservation within this superfamily, the crystal structure of the corresponding domain of an archaeal amoB subunit from Nitrosocaldus yellowstonii has been determined to 1.8 Å resolution. The structure reveals a remarkable conservation of overall fold and copper binding site location as well as several notable differences that may have implications for function and stability.


    Organizational Affiliation

    Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois, 60208.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative archaeal ammonia monooxygenase subunit B
A
166Candidatus Nitrosocaldus yellowstonensisMutation(s): 0 
Gene Names: amoB
Find proteins for B0LKZ4 (Candidatus Nitrosocaldus yellowstonensis)
Go to UniProtKB:  B0LKZ4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.796 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.886α = 90.00
b = 47.886β = 90.00
c = 192.614γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary