8IVP

Crystal structure of MV in complex with LLP and FRU from Mycobacterium vanbaalenii

• PDB DOI: https://doi.org/10.2210/pdb8IVP/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium vanbaalenii PYR-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-03-28 Released: 2024-01-24 
• Deposition Author(s): Li, Q., Zhu, Y.M., Gao, J., Wei, H.L., Han, X., Liu, W.D., Sun, Y.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.188 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Starting Model: in silico

Literature

Crystal structure of MV in complex with LLP and FRU from Mycobacterium vanbaalenii

Li, Q., Zhu, Y.M., Gao, J., Wei, H.L., Han, X., Liu, W.D., Sun, Y.X.

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: 148.25 kDa 
• Atom Count: 11,496 
• Modelled Residue Count: 1,282 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase	A, B, C, D	337	Mycolicibacterium vanbaalenii PYR-1	Mutation(s): 9  Gene Names: Mvan_4516 EC: 2.6.1
UniProt
Find proteins for A1TDP1 (Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1)) Explore A1TDP1  Go to UniProtKB:  A1TDP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth C]	D-fructose C6 H12 O6 BJHIKXHVCXFQLS-UYFOZJQFSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.188 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.707	α = 90
b = 112.243	β = 112.31
c = 92.098	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Li, Q., Zhu, Y.M., Gao, J., Wei, H.L., Han, X., Liu, W.D., Sun, Y.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release