5CLK | pdb_00005clk

Crystal structure of SZ348 in complex with S,S-cyclohexanediol

• PDB DOI: https://doi.org/10.2210/pdb5CLK/pdb

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


• Deposited: 2015-07-16 Released: 2016-07-20 
• Deposition Author(s): Wu, L., Sun, Z.T., Reetz, M.T., Zhou, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SZ348 in complex with S,S-cyclohexanediol

Wu, L., Sun, Z.T., Reetz, M.T., Zhou, J.H.

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: 35.37 kDa 
• Atom Count: 2,455 
• Modeled Residue Count: 301 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Limonene-1,2-epoxide hydrolase	A, B	155	Rhodococcus erythropolis	Mutation(s): 3  Gene Names: limA EC: 3.3.2.8
UniProt
Find proteins for Q9ZAG3 (Rhodococcus erythropolis) Explore Q9ZAG3  Go to UniProtKB:  Q9ZAG3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ZQ	F [auth A], J [auth B]	(1S,2S)-cyclohexane-1,2-diol C6 H12 O2 PFURGBBHAOXLIO-WDSKDSINSA-N
NI	C [auth A], D [auth A], E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	G [auth A], H [auth A], K [auth B], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.943	α = 90
b = 104.943	β = 90
c = 73.896	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Wu, L., Sun, Z.T., Reetz, M.T., Zhou, J.H.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description