6VOX | pdb_00006vox

Crystal structure of multi-copper oxidase from Pseudomonas Parafulva

• PDB DOI: https://doi.org/10.2210/pdb6VOX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas parafulva
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-31 Released: 2021-02-03 
• Deposition Author(s): Partowmah, S.H., Coler, E.A., Soares, A.S., Collins, R.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.258 (Depositor) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of multi-copper oxidase from Pseudomonas Parafulva

Partowmah, S., Coler, E.A., Soares, A.S., Collins, R.E.

To be published.

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: 47.56 kDa 
• Atom Count: 3,203 
• Modeled Residue Count: 407 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper oxidase	A	420	Pseudomonas parafulva	Mutation(s): 0  Gene Names: NJ69_01745

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2O (Subject of Investigation/LOI)	B [auth A]	CU-O-CU LINKAGE Cu2 O BERDEBHAJNAUOM-UHFFFAOYSA-N
CU	C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.258 (Depositor) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.35	α = 90
b = 170.35	β = 90
c = 131	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Currently 6VOX does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Partowmah, S.H., Coler, E.A., Soares, A.S., Collins, R.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM111244
Department of Energy (DOE, United States)	United States	KP1605010
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R21GM129570-01

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description