3HEJ

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb3HEJ/pdb

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

Deposited: 2009-05-08 Released: 2010-05-19
Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Heroux, A., Garcia-Moreno, E.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.244
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Domain swapping promoted by a single mutation that introduces an ionizable group into the hydrophobic core of a protein

Khangulov, V.S., Schlessman, J.L., Heroux, A., Garcia-Moreno, E.B.

To be published.

Macromolecule Content

Total Structure Weight: 66.83 kDa
Atom Count: 5,045
Modelled Residue Count: 540
Deposited Residue Count: 572
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, B [auth D], C [auth B], D [auth C]	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THP Query on THP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth D] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C]	E [auth A], H [auth D], I [auth B], K [auth C]	THYMIDINE-3',5'-DIPHOSPHATE C₁₀ H₁₆ N₂ O₁₁ P₂ CSNCBOPUCJOHLS-XLPZGREQSA-N		Interactions Focus chain E [auth A] Focus chain H [auth D] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth D] Focus chain I [auth B] Focus chain K [auth C]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C]	G [auth A], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]