5UC7 | pdb_00005uc7

Crystal structure of BioA / 7,8-diaminopelargonic acid aminotransferase / DAPA synthase from Citrobacter rodentium, PLP complex

• PDB DOI: https://doi.org/10.2210/pdb5UC7/pdb

• Classification: TRANSFERASE
• Organism(s): environmental samples
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-21 Released: 2017-01-25 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of BioA / 7,8-diaminopelargonic acid aminotransferase / DAPA synthase from Citrobacter rodentium, PLP complex

Stogios, P.J.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 48.01 kDa 
• Atom Count: 3,873 
• Modeled Residue Count: 431 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	A	431	environmental samples	Mutation(s): 0  Gene Names: bioA, ROD_07751 EC: 2.6.1.62
UniProt
Find proteins for D2TPI3 (Citrobacter rodentium (strain ICC168)) Explore D2TPI3  Go to UniProtKB:  D2TPI3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	B [auth A], C [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35uc7

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.369	α = 90
b = 88.306	β = 90
c = 63.274	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection