3TSM | pdb_00003tsm

Crystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb3TSM/pdb

• Classification: LYASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-13 Released: 2011-10-05 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis

Gardberg, A., Edwards, T., Sankaran, B., Staker, B., Stewart, L.

To be published.

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: 59.58 kDa 
• Atom Count: 4,228 
• Modeled Residue Count: 521 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indole-3-glycerol phosphate synthase	A, B	272	Brucella abortus 2308	Mutation(s): 0  Gene Names: trpC, BAB1_1164 EC: 4.1.1.48
UniProt
Find proteins for Q2YRR4 (Brucella abortus (strain 2308)) Explore Q2YRR4  Go to UniProtKB:  Q2YRR4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNL	F [auth B]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TSM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.8	α = 90
b = 73.29	β = 90
c = 118.94	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description