3SON | pdb_00003son

Crystal structure of a putativel NUDIX hydrolase (LMOf2365_2679) from Listeria monocytogenes str. 4b F2365 at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3SON/pdb

Classification: HYDROLASE
Organism(s): Listeria monocytogenes ATCC 19115
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-30 Released: 2011-08-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.196 (Depositor), 0.194 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3SON

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical NUDIX hydrolase (LMOf2365_2679) from LISTERIA MONOCYTOGENES (ATCC 19115) at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 34.88 kDa
Atom Count: 2,557
Modeled Residue Count: 293
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical NUDIX hydrolase	A, B	149	Listeria monocytogenes ATCC 19115	Mutation(s): 0 Gene Names: LMOf2365_2679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.196 (Depositor), 0.194 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data:

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.88	α = 90
b = 57.88	β = 90
c = 94.49	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary

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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.