4EEN | pdb_00004een

crystal structure of HAD FAMILY HYDROLASE DR_1622 from Deinococcus radiodurans R1 (TARGET EFI-501256) with bound magnesium

• PDB DOI: https://doi.org/10.2210/pdb4EEN/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2012-04-18 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Allen, K.N., Dunaway-Mariano, D., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HAD HYDROLASE DR_1622 Deinococcus radiodurans R1 (TARGET EFI-501256)

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Allen, K.N., Dunaway-Mariano, D., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.67 kDa 
• Atom Count: 1,938 
• Modeled Residue Count: 229 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase-related protein	A	259	Deinococcus radiodurans	Mutation(s): 0  Gene Names: DR_1622
UniProt
Find proteins for Q9RTX8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RTX8  Go to UniProtKB:  Q9RTX8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.456	α = 90
b = 55.456	β = 90
c = 274.172	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Allen, K.N., Dunaway-Mariano, D., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description