6D9N | pdb_00006d9n

Crystal structure of an organic hydroperoxide resistance protein from Elizabethkingia anophelis with crystallant-derived thiocyanate bound

• PDB DOI: https://doi.org/10.2210/pdb6D9N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Elizabethkingia anophelis NUHP1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-30 Released: 2018-06-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an organic hydroperoxide resistance protein from Elizabethkingia anophelis with crystallant-derived thiocyanate bound

Mayclin, S.J., Delker, S.L., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 31.91 kDa 
• Atom Count: 2,722 
• Modeled Residue Count: 283 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Organic hydroperoxide resistance protein	A, B	148	Elizabethkingia anophelis NUHP1	Mutation(s): 0  Gene Names: BD94_1921
UniProt
Find proteins for A0A077EDR1 (Elizabethkingia anophelis NUHP1) Explore A0A077EDR1  Go to UniProtKB:  A0A077EDR1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	C [auth A], D [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.39	α = 90
b = 50.03	β = 102.63
c = 57.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary