9FYB | pdb_00009fyb

Structural Insights into the NMN Complex of Nicotinate Nucleotide Adenylyltransferase from Enterococcus faecium via Co-Crystallization Studies

PDB DOI: https://doi.org/10.2210/pdb9FYB/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-03 Released: 2024-07-17
Deposition Author(s): Pandian, R., Jeje, O.A., Sayed, Y., Achilonu, I.A.
Funding Organization(s): Science and Technology Funding Council, South African Medical Research Council self-initiated research grant (SAMRC SIR Grant)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.268 (Depositor), 0.273 (DCC)
R-Value Work:
0.209 (Depositor), 0.222 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural Insights into the NMN Complex of Nicotinate Nucleotide Adenylyltransferase from Enterococcus faecium via Co-Crystallization Studies

Jeje, O.A., Pandian, R., Sayed, Y., Achilonu, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 50.75 kDa
Atom Count: 3,283
Modeled Residue Count: 367
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide adenylyltransferase	A, B	214	Enterococcus faecium	Mutation(s): 0 Gene Names: nadD, nadD_1, B1P95_04405, BU194_05695, DTPHA_1401727, HMPREF3199_01612 EC: 2.7.7.18
UniProt
Find proteins for A0A133MWI0 (Enterococcus faecium) Explore A0A133MWI0 Go to UniProtKB: A0A133MWI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A133MWI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMN (Subject of Investigation/LOI) Query on NMN 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]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C₁₁ H₁₆ N₂ O₈ P DAYLJWODMCOQEW-TURQNECASA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.268 (Depositor), 0.273 (DCC)
R-Value Work: 0.209 (Depositor), 0.222 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.449	α = 90
b = 107.344	β = 128.96
c = 62.344	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Technology Funding Council	United Kingdom	ST/R002754/1
South African Medical Research Council self-initiated research grant (SAMRC SIR Grant)	South Africa	ACHL019