6JHU | pdb_00006jhu

Crystal Structure Of Biotin Protein Ligase From Leishmania Major in complex with Biotinyl-5-AMP

• PDB DOI: https://doi.org/10.2210/pdb6JHU/pdb

• Classification: LIGASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-19 Released: 2020-04-08 
• Deposition Author(s): Rajak, M., Patel, A., Sundd, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Models: experimental

Literature

Leishmania major biotin protein ligase forms a unique cross-handshake dimer

Rajak, M., Bhatnagar, S., Pandey, S., Kumar, S., Verma, S., Patel, A.K., Sundd, M.

(2021) Acta Crystallogr D Biol Crystallogr 77

• DOI: https://doi.org/10.1107/S2059798321001418

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: 31.23 kDa 
• Atom Count: 1,923 
• Modeled Residue Count: 248 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin/lipoate protein ligase-like protein	A	283	Leishmania major	Mutation(s): 0  Gene Names: LMJF_31_1070 EC: 6.3.4.15
UniProt
Find proteins for Q4Q6F6 (Leishmania major) Explore Q4Q6F6  Go to UniProtKB:  Q4Q6F6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BT5 (Subject of Investigation/LOI)	B [auth A]	BIOTINYL-5-AMP C20 H28 N7 O9 P S UTQCSTJVMLODHM-RHCAYAJFSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.848	α = 90
b = 46.621	β = 104.569
c = 54.573	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data collection
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Rajak, M., Patel, A., Sundd, M.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Derived calculations
• Version 1.2: 2021-04-14
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description