3S9W

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G bound to Ca2+ and thymidine-5',3'-diphosphate at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb3S9W/pdb

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

Deposited: 2011-06-02 Released: 2011-06-22
Deposition Author(s): Doctrow, B.M., Schlessman, J.L., Garcia-Moreno E., B., Heroux, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G bound to Ca2+ and thymidine-5',3'-diphosphate at cryogenic temperature

Doctrow, B.M., Schlessman, J.L., Garcia-Moreno E., B.

To be published.

Macromolecule Content

Total Structure Weight: 16.51 kDa
Atom Count: 1,205
Modelled Residue Count: 129
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	143	Staphylococcus aureus	Mutation(s): 6 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00644
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THP Query on THP 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]	THYMIDINE-3',5'-DIPHOSPHATE C₁₀ H₁₆ N₂ O₁₁ P₂ CSNCBOPUCJOHLS-XLPZGREQSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.207	α = 90
b = 60.531	β = 93.13
c = 38.354	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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3S9W

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G bound to Ca2+ and thymidine-5',3'-diphosphate at cryogenic temperature

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G bound to Ca2+ and thymidine-5',3'-diphosphate at cryogenic temperature

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)