3P52

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

PDB DOI: https://doi.org/10.2210/pdb3P52/pdb

Classification: LIGASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-07 Released: 2010-10-27
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Skarina, T., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.245
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Skarina, T., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 56.43 kDa
Atom Count: 3,659
Modelled Residue Count: 458
Deposited Residue Count: 498
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	249	Campylobacter jejuni	Mutation(s): 0 Gene Names: Cj0810, nadE EC: 6.3.1.5
UniProt
Find proteins for Q9PPB0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB0 Go to UniProtKB: Q9PPB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PPB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	C [auth A], D [auth B], E [auth B], F [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [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: 2.74 Å
R-Value Free: 0.245
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 3 2 1
Diffraction Data: https://doi.org/10.18430/M33P52

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.945	α = 90
b = 120.945	β = 90
c = 91.795	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection

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Help and Resources

3P52

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)