9CII | pdb_00009cii

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D/L36R at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb9CII/pdb

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

Deposited: 2024-07-03 Released: 2024-08-07
Deposition Author(s): Zhang, Y., Schlessman, J.L., Robinson, A.C., 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: 1.85 Å
R-Value Free:
0.209 (Depositor), 0.213 (DCC)
R-Value Work:
0.166 (Depositor), 0.175 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D/L36R at cryogenic temperature

Zhang, Y., Schlessman, J.L., Robinson, A.C., Garcia-Moreno E., B.

To be published.

Macromolecule Content

Total Structure Weight: 16.65 kDa
Atom Count: 1,238
Modeled Residue Count: 129
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	143	Staphylococcus aureus	Mutation(s): 2 Gene Names: nuc, SACOL0860 EC: 3.1.31.1
UniProt
Find proteins for Q5HHM4 (Staphylococcus aureus (strain COL)) Explore Q5HHM4 Go to UniProtKB: Q5HHM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HHM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THP (Subject of Investigation/LOI) Query on THP 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]	THYMIDINE-3',5'-DIPHOSPHATE C₁₀ H₁₆ N₂ O₁₁ P₂ CSNCBOPUCJOHLS-XLPZGREQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.209 (Depositor), 0.213 (DCC)
R-Value Work: 0.166 (Depositor), 0.175 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.172	α = 90
b = 60.277	β = 93.69
c = 38.35	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

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	GM 061597

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release

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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.