3HEJ | pdb_00003hej

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 (Depositor), 0.239 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (Depositor)

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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
Modeled Residue Count: 540
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain I [auth B] mmCIF 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]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF 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]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF 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]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.244 (Depositor), 0.239 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.598	α = 90
b = 74.42	β = 90.22
c = 67.975	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-05-19

Deposition Author(s):

Khangulov, V.S.

Schlessman, J.L.

Garcia-Moreno, E.B.

Revision History (Full details and data files)

Version 1.0: 2010-05-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

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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.