6EEK | pdb_00006eek

Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb6EEK/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-08-14 Released: 2018-08-29
Deposition Author(s): Kougentakis, C.M., Schlessman, J.L., Garcia-Moreno, E.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.309 (Depositor), 0.308 (DCC)
R-Value Work:
0.254 (Depositor), 0.259 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature

Kougentakis, C.M., Schlessman, J.L., Garcia-Moreno, E.B.

To be published.

Macromolecule Content

Total Structure Weight: 16.2 kDa
Atom Count: 971
Modeled Residue Count: 119
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	143	Staphylococcus aureus	Mutation(s): 7 Gene Names: nuc EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644 Go to UniProtKB: P00644
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00644
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.309 (Depositor), 0.308 (DCC)
R-Value Work: 0.254 (Depositor), 0.259 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.795	α = 90
b = 71.795	β = 90
c = 56.804	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Kougentakis, C.M.

Schlessman, J.L.

Garcia-Moreno, E.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM061597

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-11
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.