7C23

Crystal structure of CrmE10, a SGNH-hydrolase family esterase

• PDB DOI: https://doi.org/10.2210/pdb7C23/pdb
• Entry: 7C23 supersedes: 6M41

• Classification: HYDROLASE
• Organism(s): Croceicoccus marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-07 Released: 2020-05-20 
• Deposition Author(s): Li, Z., Li, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structure-guided protein engineering increases enzymatic activities of the SGNH family esterases.

Li, Z., Li, L., Huo, Y., Chen, Z., Zhao, Y., Huang, J., Jian, S., Rong, Z., Wu, D., Gan, J., Hu, X., Li, J., Xu, X.W.

(2020) Biotechnol Biofuels 13: 107-107

• PubMed: 32549911 
• DOI: https://doi.org/10.1186/s13068-020-01742-8
• Primary Citation of Related Structures:  
  7C23, 7C29, 7C82, 7C84, 7C85


• PubMed Abstract: 
  

  Esterases and lipases hydrolyze short-chain esters and long-chain triglycerides, respectively, and therefore play essential roles in the synthesis and decomposition of ester bonds in the pharmaceutical and food industries. Many SGNH family esterases share high similarity in sequences. However, they have distinct enzymatic activities toward the same substrates. Due to a lack of structural information, the detailed catalytic mechanisms of these esterases remain barely investigated.

---

Organizational Affiliation: 

State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.4 kDa 
• Atom Count: 3,339 
• Modelled Residue Count: 388 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase	A, B	205	Croceicoccus marinus	Mutation(s): 0  Gene Names: A9D14_03620
UniProt
Find proteins for A0A1Z1F9L9 (Croceicoccus marinus) Explore A0A1Z1F9L9  Go to UniProtKB:  A0A1Z1F9L9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	J [auth A], O [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	I [auth A], L [auth B], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.655	α = 90
b = 37.019	β = 99.055
c = 99.747	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Li, Z., Li, J.
• This entry supersedes: 6M41

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500600

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description