5HXX | pdb_00005hxx

Crystal structure of AspAT from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb5HXX/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-31 Released: 2016-02-24 
• Deposition Author(s): Son, H.-F., Kim, K.-J.
• Funding Organization(s): National Research Foundation of Korea

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structural insights into a novel class of aspartate aminotransferase from Corynebacterium glutamicum

Son, H.-F., Kim, K.-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: 95.85 kDa 
• Atom Count: 7,384 
• Modeled Residue Count: 847 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE AMINOTRANSFERASE	A, B	432	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: aspB, cg0294 EC: 2.6.1.1
UniProt
Find proteins for Q8NTR2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NTR2  Go to UniProtKB:  Q8NTR2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	C [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
PLP	F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLU	G [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
AKG	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.388	α = 90
b = 53.521	β = 104.23
c = 170.224	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Son, H.-F., Kim, K.-J.

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Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	2014R1A2A2A01005752
National Research Foundation of Korea	Korea, Republic Of	2014M1M2M2033626
National Research Foundation of Korea	Korea, Republic Of	2015H1A2A1034233

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description