3UMB | pdb_00003umb

Crystal Structure of the L-2-Haloacid Dehalogenase RSc1362

• PDB DOI: https://doi.org/10.2210/pdb3UMB/pdb

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


• Deposited: 2011-11-12 Released: 2012-11-14 
• Deposition Author(s): Petit, P., Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural adaptations of L-2-haloacid dehalogenases that enable hydrolytic defluorination

Chan, P.W.Y., To, T.K.W., Petit, P., Tran, C., Waelti, M., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

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: 26.21 kDa 
• Atom Count: 1,828 
• Modelled Residue Count: 227 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dehalogenase-like hydrolase	A	233	Ralstonia solanacearum	Mutation(s): 0  Gene Names: RSc1362 EC: 3.8.1.2
UniProt
Find proteins for Q8XZN3 (Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)) Explore Q8XZN3  Go to UniProtKB:  Q8XZN3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 129.57	β = 90
c = 54.3	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Petit, P., Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary