8JUS

Crystal structure of aspartate semialdehyde dehydrogenase from Porphyromonas gingivalis complexed with 2',5'adenosine diphosphate

PDB DOI: https://doi.org/10.2210/pdb8JUS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Porphyromonas gingivalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-27 Released: 2024-06-05
Deposition Author(s): Hwang, J., Do, H., Lee, J.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.185

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

Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Porphyromonas gingivalis.

Hwang, J., Do, H., Shim, Y.S., Lee, J.H.

(2023) Crystals (Basel) 13

DOI: https://doi.org/10.3390/cryst13081274

Macromolecule Content

Total Structure Weight: 75.45 kDa
Atom Count: 5,669
Modelled Residue Count: 670
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate-semialdehyde dehydrogenase	A, B	337	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: asd, PGIN_13-1_01585 EC: 1.2.1.11
UniProt
Find proteins for A0AAF0BGE9 (Porphyromonas gingivalis) Explore A0AAF0BGE9 Go to UniProtKB: A0AAF0BGE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAF0BGE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2P (Subject of Investigation/LOI) Query on A2P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	ADENOSINE-2'-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ AEOBEOJCBAYXBA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.99	α = 90
b = 108.22	β = 90
c = 160.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	PM23030

Revision History (Full details and data files)

Version 1.0: 2024-06-05
Type: Initial release

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.