6LE2

Structure of D-carbamoylase mutant from Nitratireductor indicus

• PDB DOI: https://doi.org/10.2210/pdb6LE2/pdb

• Classification: HYDROLASE
• Organism(s): Nitratireductor indicus C115
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-11-23 Released: 2020-10-28 
• Deposition Author(s): Ni, Y., Liu, Y.F., Xu, G.C., Dai, W.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Engineering of D-Carbamoylase Reveals a Key Loop at Substrate Entrance Tunnel

Liu, Y., Xu, G., Zhou, J., Ni, J., Zhang, L., Hou, X., Yin, D., Rao, Y., Zhao, Y.L., Ni, Y.

(2020) ACS Catal 10: 12393-12402

• DOI: https://doi.org/10.1021/acscatal.0c02942

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: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 71.86 kDa 
• Atom Count: 5,196 
• Modelled Residue Count: 615 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-carbamoyl-D-amino-acid hydrolase	A, B	316	Nitratireductor indicus C115	Mutation(s): 4  Gene Names: NA8A_19058
UniProt
Find proteins for K2NMS4 (Nitratireductor indicus C115) Explore K2NMS4  Go to UniProtKB:  K2NMS4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.32	α = 90
b = 95.32	β = 90
c = 258.57	γ = 120

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: 2020-10-28 
Deposition Author(s): Ni, Y., Liu, Y.F., Xu, G.C., Dai, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2021-05-12
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description