4RNC | pdb_00004rnc

Crystal structure of an esterase RhEst1 from Rhodococcus sp. ECU1013

• PDB DOI: https://doi.org/10.2210/pdb4RNC/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. ECU1013
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-23 Released: 2015-10-28 
• Deposition Author(s): Dou, S., Kong, X.D., Xu, J.H., Zhou, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Substrate channel evolution of an esterase for the synthesis of Cilastatin

Luan, Z.J., L Li, F., Dou, S., Chen, Q., Kong, X.D., Zhou, J., Yu, H.L., Xu, J.H.

(2015) Catal Sci Technol 5: 2622-2629

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: 97.58 kDa 
• Atom Count: 6,672 
• Modeled Residue Count: 831 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C	310	Rhodococcus sp. ECU1013	Mutation(s): 0  EC: 3.1.1.1
UniProt
Find proteins for A0A088CB91 (Rhodococcus sp. ECU1013) Explore A0A088CB91  Go to UniProtKB:  A0A088CB91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.926	α = 90
b = 45.383	β = 105.82
c = 77.443	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Dou, S., Kong, X.D., Xu, J.H., Zhou, J.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations