4BXV | pdb_00004bxv

Three-dimensional structure of the mutant K109A of Paracoccus pantotrophus pseudoazurin at pH 7.0

• PDB DOI: https://doi.org/10.2210/pdb4BXV/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Paracoccus pantotrophus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-07-15 Released: 2014-07-30 
• Deposition Author(s): Freire, F., Mestre, A., Pinho, J., Najmudin, S., Bonifacio, C., Pauleta, S.R., Romao, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.317 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Model: experimental

Literature

Exploring the Surface Determinants of Paracoccus Pantotrophus Pseudoazurin

Freire, F., Mestre, A., Pinho, J., Najmudin, S., Bonifacio, C., Pauleta, S.R., Romao, M.J.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.11 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PSEUDOAZURIN	A, B	123	Paracoccus pantotrophus	Mutation(s): 1
UniProt
Find proteins for P80401 (Paracoccus pantotrophus) Explore P80401  Go to UniProtKB:  P80401

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.317 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.31	α = 90
b = 71.72	β = 90
c = 91.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Freire, F., Mestre, A., Pinho, J., Najmudin, S., Bonifacio, C., Pauleta, S.R., Romao, M.J.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description