4NPO | pdb_00004npo

Crystal structure of protein with unknown function from Deinococcus radiodurans at P61 spacegroup

• PDB DOI: https://doi.org/10.2210/pdb4NPO/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-22 Released: 2013-12-11 
• Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Shabalin, I.G., Shumilin, I.A., Dorovatovsky, P.V., Lipkin, A.V., Popov, V.O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of protein with unknown function at P61 spacegroup

Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Shabalin, I.G., Shumilin, I.A., Dorovatovsky, P.V., Lipkin, A.V., Popov, V.O.

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: 28.04 kDa 
• Atom Count: 1,912 
• Modeled Residue Count: 207 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	125	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
ACE	H [auth B], I [auth B]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.39	α = 90
b = 80.39	β = 90
c = 69.92	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Rakitina, T.V., Korgenevsky, D.A., Shabalin, I.G., Shumilin, I.A., Dorovatovsky, P.V., Lipkin, A.V., Popov, V.O.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description