5F23

Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb5F23/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-12-01 Released: 2015-12-23
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.180
R-Value Work: 0.138
R-Value Observed: 0.140

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD

Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 31.62 kDa
Atom Count: 2,401
Modelled Residue Count: 263
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A	283	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: nadE, PA4920 EC: 6.3.1.5
UniProt
Find proteins for Q9HUP3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUP3 Go to UniProtKB: Q9HUP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HUP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.180
R-Value Work: 0.138
R-Value Observed: 0.140
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M35F23

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.87	α = 90
b = 41.19	β = 113.54
c = 64.13	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-23

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-12-23
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5F23

Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD

Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)