6LE2 | pdb_00006le2

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.229 (Depositor), 0.233 (DCC)
R-Value Work:
0.180 (Depositor), 0.186 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K2NMS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.229 (Depositor), 0.233 (DCC)
R-Value Work: 0.180 (Depositor), 0.186 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

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

Revision History (Full details and data files)

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

6LE2 | pdb_00006le2

Structure of D-carbamoylase mutant from Nitratireductor indicus

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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