4CF3 | pdb_00004cf3

Mutagenesis of a Rhodobacteraceae L-haloacid dehalogenase

• PDB DOI: https://doi.org/10.2210/pdb4CF3/pdb

• Classification: HYDROLASE
• Organism(s): Paracoccaceae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-11-13 Released: 2014-11-26 
• Deposition Author(s): Novak, H.R., Sayer, C., Isupov, M.N., Littlechild, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Mutagenesis of a Rhodobacteraceae L-Haloacid Dehalogenase

Novak, H.R., Sayer, C., Isupov, M.N., Littlechild, J.A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 103.44 kDa 
• Atom Count: 7,282 
• Modeled Residue Count: 903 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-HALOACID DEHALOGENASE	A, B, C, D	236	Paracoccaceae	Mutation(s): 1  EC: 3.8.1.2
UniProt
Find proteins for R4GRT2 (Paracoccaceae) Explore R4GRT2  Go to UniProtKB:  R4GRT2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A], F [auth B], G [auth C], H [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ASB	A, B, C, D	L-PEPTIDE LINKING	C6 H9 N O6		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.17	α = 90
b = 68.27	β = 90
c = 283.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Novak, H.R., Sayer, C., Isupov, M.N., Littlechild, J.A.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description