6LCG | pdb_00006lcg

Structure of D-carbamoylase mutant from Nitratireductor indicus

PDB DOI: https://doi.org/10.2210/pdb6LCG/pdb

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

Deposited: 2019-11-18 Released: 2020-10-28
Deposition Author(s): Liu, Y.F., Ni, Y., Xu, G.C., Dai, W.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.266 (Depositor), 0.268 (DCC)
R-Value Work:
0.216 (Depositor), 0.219 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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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: 69.51 kDa
Atom Count: 4,849
Modeled Residue Count: 604
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-carbamoyl-D-amino-acid hydrolase	A, B	307	Nitratireductor indicus C115	Mutation(s): 3 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266 (Depositor), 0.268 (DCC)
R-Value Work: 0.216 (Depositor), 0.219 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.65	α = 90
b = 95.65	β = 90
c = 261.621	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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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.