5LIZ | pdb_00005liz

The structure of Nt.BspD6I nicking endonuclease with all cysteines mutated by serine residues at 0.19 nm resolution .

PDB DOI: https://doi.org/10.2210/pdb5LIZ/pdb

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

Deposited: 2016-07-16 Released: 2017-08-02
Deposition Author(s): Kachalova, G.S., Artyukh, R.I., Perevyazova, T.A., Yunusova, A.K., Popov, A.N., Bartunik, H.D., Zheleznaya, L.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.207 (Depositor), 0.213 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural features of Cysteine residues mutation 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: 71.73 kDa
Atom Count: 5,062
Modeled Residue Count: 584
Deposited Residue Count: 610
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicking endonuclease N.BspD6I	A	610	Bacillus sp. (in: firmicutes)	Mutation(s): 4
UniProt
Find proteins for A0ACD6B9F6 (Bacillus sp) Explore A0ACD6B9F6 Go to UniProtKB: A0ACD6B9F6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.239 (Depositor), 0.243 (DCC)
R-Value Work: 0.207 (Depositor), 0.213 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.867	α = 90
b = 93.059	β = 112.89
c = 76.58	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Kachalova, G.S.

Perevyazova, T.A.

Zheleznaya, L.A.

Revision History (Full details and data files)

Version 1.0: 2017-08-02
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.