8I78 | pdb_00008i78

Meso-Diaminopimelate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb8I78/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Proteus vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-31 Released: 2024-02-07 
• Deposition Author(s): Wei, S., Wu, T.F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope

wu, T.F., wei, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 129.1 kDa 
• Atom Count: 9,445 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate D-dehydrogenase	A, B, C, D	299	Proteus vulgaris	Mutation(s): 0  Gene Names: EKQ45_05540 EC: 1.4.1.16
UniProt
Find proteins for A0A379F6K8 (Proteus vulgaris) Explore A0A379F6K8  Go to UniProtKB:  A0A379F6K8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.91	α = 90
b = 211.91	β = 90
c = 245.76	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Wei, S., Wu, T.F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release