8JUO | pdb_00008juo

Crystal structure of aspartate semialdehyde dehydrogenase from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb8JUO/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: in silico

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.6 kDa 
• Atom Count: 5,542 
• Modeled Residue Count: 670 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.86	α = 90
b = 108.86	β = 90
c = 162.07	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Hwang, J., Do, H., Lee, J.H.

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

Revision History  

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