4FB7 | pdb_00004fb7

The apo form of idole-3-glycerol phosphate synthase (TrpC) form Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4FB7/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-22 Released: 2012-06-13 
• Deposition Author(s): Michalska, K., Chhor, G., Jedrzejczak, R., Terwilliger, T.C., Rubin, E.J., Guinn, K., Baker, D., Ioerger, T.R., Sacchettini, J.C., Joachimiak, A., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI), Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.154 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

The apo form of idole-3-glycerol phosphate synthase (TrpC) form Mycobacterium tuberculosis

Michalska, K., Chhor, G., Jedrzejczak, R., Terwilliger, T.C., Rubin, E.J., Guinn, K., Baker, D., Ioerger, T.R., Sacchettini, J.C., Joachimiak, A., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI), Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.82 kDa 
• Atom Count: 2,358 
• Modeled Residue Count: 266 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indole-3-glycerol phosphate synthase	A	275	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: MT1646, MTCY01B2.03, Rv1611, trpC EC: 4.1.1.48
UniProt
Find proteins for P9WFX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX7  Go to UniProtKB:  P9WFX7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.154 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34FB7

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.638	α = 90
b = 58.504	β = 90
c = 80.168	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Michalska, K., Chhor, G., Jedrzejczak, R., Terwilliger, T.C., Rubin, E.J., Guinn, K., Baker, D., Ioerger, T.R., Sacchettini, J.C., Joachimiak, A., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI), Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary