4O65 | pdb_00004o65

Crystal structure of the cupredoxin domain of amoB from Nitrosocaldus yellowstonii

• PDB DOI: https://doi.org/10.2210/pdb4O65/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candidatus Nitrosocaldus yellowstonensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-20 Released: 2014-04-02 
• Deposition Author(s): Lawton, T.J., Ham, J., Sun, T., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

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

• PubMed: 24523098 
• DOI: https://doi.org/10.1002/prot.24535
• Primary Citation Related Structures: 
  4O65


• 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 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.

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Organizational Affiliation: 
• Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois, 60208.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.41 kDa 
• Atom Count: 1,364 
• Modeled Residue Count: 153 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative archaeal ammonia monooxygenase subunit B	A	166	Candidatus Nitrosocaldus yellowstonensis	Mutation(s): 0  Gene Names: amoB
UniProt
Find proteins for B0LKZ4 (Candidatus Nitrosocaldus yellowstonensis) Explore B0LKZ4  Go to UniProtKB:  B0LKZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.886	α = 90
b = 47.886	β = 90
c = 192.614	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Lawton, T.J., Ham, J., Sun, T., Rosenzweig, A.C.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-09-03
  Changes: Database references
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary