8ISC

Crystal structure of MV in complex with LLP

• PDB DOI: https://doi.org/10.2210/pdb8ISC/pdb

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


• Deposited: 2023-03-20 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: 2.27 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of MV in complex with LLP

Li, Q., Liu, W.D.

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: 147.53 kDa 
• Atom Count: 11,081 
• Modelled Residue Count: 1,280 
• 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

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: 2.27 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.95	α = 90
b = 112.85	β = 112.37
c = 92.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing
XDS	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