2IN3 | pdb_00002in3

Crystal structure of a putative protein disulfide isomerase from Nitrosomonas europaea

• PDB DOI: https://doi.org/10.2210/pdb2IN3/pdb

• Classification: ISOMERASE
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-10-05 Released: 2006-11-21 
• Deposition Author(s): Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of a putative protein disulfide isomerase from Nitrosomonas europaea

Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.88 kDa 
• Atom Count: 1,867 
• Modeled Residue Count: 204 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	216	Nitrosomonas europaea	Mutation(s): 4  Gene Names: NE2553
UniProt
Find proteins for Q82S11 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82S11  Go to UniProtKB:  Q82S11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.844	α = 90
b = 59.642	β = 90
c = 84.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
autoSHARP	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary