4E6I | pdb_00004e6i

Crystal structure of Staphylococcal nuclease variant NVIAGA V99G at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb4E6I/pdb

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

Deposited: 2012-03-15 Released: 2012-04-18
Deposition Author(s): Doctrow, B.M., Schlessman, J.L., Garcia-Moreno E., B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.268 (Depositor), 0.233 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.217 (Depositor)

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

Literature

Local flexibility as a determinant of pKa values of surface ionizable groups in proteins

Doctrow, B.M., Schlessman, J.L., Garcia-Moreno E., B., Baran, K.L., Chimenti, M.S., Herbst, K.J., Fitch, C.A., Majumdar, A.

To be published.

Macromolecule Content

Total Structure Weight: 33.69 kDa
Atom Count: 2,082
Modeled Residue Count: 247
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A, B	149	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.268 (Depositor), 0.233 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.337	α = 90
b = 68.337	β = 90
c = 63.227	γ = 90

Software Package:

Software Name	Purpose
XPREP	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
APEX	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

Schlessman, J.L.

Garcia-Moreno E., B.

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.