3EZ0 | pdb_00003ez0

Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EZ0/pdb

• Classification: structural genomics, unknown function
• Organism(s): Arthrobacter sp. FB24
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-22 Released: 2008-11-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 101.51 kDa 
• Atom Count: 6,854 
• Modeled Residue Count: 847 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein with ferritin-like fold	A, B, C, D	225	Arthrobacter sp. FB24	Mutation(s): 0  Gene Names: YP_832262.1, Arth_2783
UniProt
Find proteins for A0ACD6B8D1 (Arthrobacter sp. (strain FB24)) Explore A0ACD6B8D1  Go to UniProtKB:  A0ACD6B8D1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	F [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	E [auth A], G [auth B], I [auth C], J [auth D]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EZ0

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 96.71	β = 97.6
c = 71.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary