5EJG | pdb_00005ejg

Crystal structure of NAD kinase P252D mutant from Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb5EJG/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-11-01 Released: 2016-11-09
Deposition Author(s): Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.324 (Depositor), 0.331 (DCC)
R-Value Work:
0.217 (Depositor), 0.232 (DCC)
R-Value Observed:
0.221 (Depositor)

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

Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes: P252D mutant

Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.

To be published.

Macromolecule Content

Total Structure Weight: 124.25 kDa
Atom Count: 7,671
Modeled Residue Count: 977
Deposited Residue Count: 1,088
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase 1	A, B, C, D	272	Listeria monocytogenes	Mutation(s): 1 Gene Names: nadK1, lmo0968 EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8D7 Go to UniProtKB: Q8Y8D7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y8D7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.324 (Depositor), 0.331 (DCC)
R-Value Work: 0.217 (Depositor), 0.232 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.217	α = 90
b = 119.655	β = 100.92
c = 68.624	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Poncet-Montange, G.

Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence, Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, 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.