3E8O | pdb_00003e8o

CRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE (DR_2100) FROM DEINOCOCCUS RADIODURANS AT 1.40 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3E8O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-20 Released: 2008-09-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.163 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

Crystal structure of protein of unknown function with ferredoxin-like fold (NP_295823.1) from DEINOCOCCUS RADIODURANS at 1.40 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)

Macromolecule Content 

• Total Structure Weight: 26.46 kDa 
• Atom Count: 1,872 
• Modeled Residue Count: 203 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein with ferredoxin-like fold	A, B	119	Deinococcus radiodurans	Mutation(s): 0  Gene Names: NP_295823.1, DR_2100
UniProt
Find proteins for Q9RSM4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RSM4  Go to UniProtKB:  Q9RSM4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	C [auth A], D [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.163 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33E8O

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.715	α = 90
b = 59.639	β = 97.18
c = 47.511	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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: 2024-10-30
  Changes: Data collection, Structure summary