3BT5

Crystal structure of DUF305 fragment from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb3BT5/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-27 Released: 2008-01-15 
• Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Rutter, M., Toro, R., Bain, K., Meyer, A.J., Powell, A., Gheyi, T., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Crystal structure of DUF305 fragment from Deinococcus radiodurans.

Ramagopal, U.A., Patskovsky, Y., Rutter, M., Toro, R., Bain, K., Meyer, A.J., Powell, A., Gheyi, T., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 19.8 kDa 
• Atom Count: 1,409 
• Modelled Residue Count: 151 
• Deposited Residue Count: 177 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein DUF305	A	177	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_1099
UniProt
Find proteins for Q9RVD0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RVD0  Go to UniProtKB:  Q9RVD0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.69	α = 90
b = 49.69	β = 90
c = 71.191	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Rutter, M., Toro, R., Bain, K., Meyer, A.J., Powell, A., Gheyi, T., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-01-15
  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: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Refinement description