4R8D | pdb_00004r8d

Crystal structure of Rv1600 encoded aminotransferase in complex with PLP-MES from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4R8D/pdb

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


• Deposited: 2014-09-01 Released: 2015-09-02 
• Deposition Author(s): Nasir, N., Anant, A., Vyas, R., Biswal, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Rv1600 encoded aminotransferase in complex with PLP-MES from Mycobacterium tuberculosis

Nasir, N., Anant, A., Vyas, R., Biswal, B.K.

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: 85.83 kDa 
• Atom Count: 5,886 
• Modeled Residue Count: 734 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidinol-phosphate aminotransferase	A, B	394	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: hisC, P425_01659, RVBD_1600 EC: 2.6.1.9
UniProt
Find proteins for P9WML7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WML7  Go to UniProtKB:  P9WML7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MES	D [auth A], I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.525	α = 90
b = 101.523	β = 90
c = 114.947	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Nasir, N., Anant, A., Vyas, R., Biswal, B.K.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description