5LHC | pdb_00005lhc

The structure of D456A mutant of Nt.BspD6I nicking endonuclease at 0.24 nm resolution .

PDB DOI: https://doi.org/10.2210/pdb5LHC/pdb
Entry: 5LHC supersedes: 4WL5

Classification: HYDROLASE
Organism(s): Bacillus sp. (in: firmicutes)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-07-10 Released: 2017-08-16
Deposition Author(s): Kachalova, G.S., Yunusova, A.K., Popov, A.N., Artyukh, R.I., Perevyazova, T.A., Bartunik, H.D., Zheleznaya, L.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.265 (Depositor), 0.265 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LHC

This is version 1.1 of the entry. See complete history.

Literature

Structural implication of activity loss by D456A mutant of the nicking endonuclease Nt.BspD6I.

Kachalova, G.S., Yunusova, A.K., Popov, A.N., Artyukh, R.I., Perevyazova, T.A., Bartunik, H.D., Zheleznaya, L.A.

To be published.

Macromolecule Content

Total Structure Weight: 144.06 kDa
Atom Count: 9,854
Modeled Residue Count: 1,161
Deposited Residue Count: 1,220
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicking endonuclease N.BspD6I	A, B	610	Bacillus sp. (in: firmicutes)	Mutation(s): 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.265 (Depositor), 0.265 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 92.666	β = 105.75
c = 113.969	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Kachalova, G.S.

Perevyazova, T.A.

Zheleznaya, L.A.

This entry supersedes: 4WL5

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2024-01-10
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.