1XNG

Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

PDB DOI: https://doi.org/10.2210/pdb1XNG/pdb

Classification: LIGASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-10-05 Released: 2005-04-05
Deposition Author(s): Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.257
R-Value Work: 0.229
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

(2005) Proteins 58: 985-988

PubMed: 15645437 Search on PubMed
DOI: https://doi.org/10.1002/prot.20377
Primary Citation of Related Structures:
1XNG, 1XNH

Organizational Affiliation

Department of Life Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.

Macromolecule Content

Total Structure Weight: 63.15 kDa
Atom Count: 4,457
Modelled Residue Count: 517
Deposited Residue Count: 536
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, B	268	Helicobacter pylori	Mutation(s): 0 EC: 6.3.1.5
UniProt
Find proteins for O25096 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25096 Go to UniProtKB: O25096
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25096
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DND Query on DND Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	NICOTINIC ACID ADENINE DINUCLEOTIDE C₂₁ H₂₇ N₆ O₁₅ P₂ SENPVEZBRZQVST-HISDBWNOSA-O		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.257
R-Value Work: 0.229
R-Value Observed: 0.232
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.403	α = 90
b = 63.403	β = 90
c = 125.688	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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1XNG

Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Entity ID: 1

UniProt

Entity Groups

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)