5CK6 | pdb_00005ck6

Crystal structure of SZ348 in complex with cyclopentene oxide

• PDB DOI: https://doi.org/10.2210/pdb5CK6/pdb

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


• Deposited: 2015-07-15 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: 2.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SZ348 in complex with cyclopentene oxide

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: 35.13 kDa 
• Atom Count: 2,431 
• Modeled Residue Count: 300 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ZS	C [auth A], H [auth B]	(1R,5S)-6-oxabicyclo[3.1.0]hexane C5 H8 O GJEZBVHHZQAEDB-SYDPRGILSA-N
NI	E [auth A], F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	D [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.159	α = 90
b = 104.159	β = 90
c = 73.625	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	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