5YHV | pdb_00005yhv

Crystal structure of an aminotransferase from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5YHV/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis
• Mutation(s): No 


• Deposited: 2017-09-30 Released: 2018-10-10 
• Deposition Author(s): Saroj, D.C., Biswal, B.K.
• Funding Organization(s): Department of Biotechnology, India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an aminotransferase from Mycobacterium tuberculosis

Saroj, D.C., Biswal, B.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 169.47 kDa 
• Atom Count: 11,078 
• Modeled Residue Count: 1,529 
• Deposited Residue Count: 1,576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B, C, D	394	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: aspB, Rv3565 EC: 2.6.1 (PDB Primary Data), 2.6.1.66 (UniProt)
UniProt
Find proteins for P96847 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96847  Go to UniProtKB:  P96847

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.277	α = 90
b = 98.224	β = 90
c = 198.774	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Saroj, D.C., Biswal, B.K.

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Funding Organization	Location	Grant Number
Department of Biotechnology, India	India	--

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary