3TEV | pdb_00003tev

The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1

• PDB DOI: https://doi.org/10.2210/pdb3TEV/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-15 Released: 2011-08-31 
• Deposition Author(s): Chang, C., Hatzos-Skintges, C., Kohler, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1

Chang, C., Hatzos-Skintges, C., Kohler, M., Clancy, S., Joachimiak, A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 76.14 kDa 
• Atom Count: 4,984 
• Modeled Residue Count: 626 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hyrolase, family 3	A, B	351	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_1333
UniProt
Find proteins for Q9RUP9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUP9  Go to UniProtKB:  Q9RUP9

Small Molecules

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: 2.30 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.841	α = 90
b = 146.841	β = 90
c = 108.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Chang, C., Hatzos-Skintges, C., Kohler, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary