4XTU | pdb_00004xtu

Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor (N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide)

• PDB DOI: https://doi.org/10.2210/pdb4XTU/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-24 Released: 2016-01-13 
• Deposition Author(s): De la Mora-Rey, T., Finzel, B.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor (N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide)

Bockman, M.R., Kalinda, A.S., Petrelli, R., De la Mora-Rey, T., Tawari, D., Liu, F., Schnappinger, D., Finzel, B.C., Aldrich, C.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.21 kDa 
• Atom Count: 4,641 
• Modeled Residue Count: 527 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional ligase/repressor BirA	A, B	270	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_01710, IQ44_01750, IQ45_01765, IQ46_01705, IQ47_01735, IQ48_01770, IU12_01860, IU13_01785, IU14_01730, IU16_01770, IU17_01745, IU18_01730, IU19_01775, IU20_01750, IU22_01755, IU23_01750, IU24_01735, IZ84_17515, JE53_17495, LJ70_17695, T209_01770 EC: 6.3.4.15
UniProt
Find proteins for I6YFP0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6YFP0  Go to UniProtKB:  I6YFP0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
44J	C [auth A], D [auth B]	N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide C21 H31 N9 O6 S2 HTTJGHVBXHXTNE-INFCYNJXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.684	α = 90
b = 68.735	β = 90
c = 115.282	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): De la Mora-Rey, T., Finzel, B.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI091790-01

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description