5CC5 | pdb_00005cc5

Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 1H-indole-3-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb5CC5/pdb

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


• Deposited: 2015-07-01 Released: 2016-08-10 
• Deposition Author(s): Huang, H.-L., Sacchettini, J.C.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal structures of fragment-bound malate synthase from Mycobacterium tuberculosis provide insights into mechanism and potential inhibitor designs

Huang, H.-L., Krieger, I.V., Gawandi, V.B., Parai, M., Sacchettini, J.C.

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: 80.74 kDa 
• Atom Count: 6,126 
• Modelled Residue Count: 709 
• Deposited Residue Count: 741 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate synthase G	A	741	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: glcB, Rv1837c, MTCY1A11.06 EC: 2.3.3.9
UniProt
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK17  Go to UniProtKB:  P9WK17

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ICO	E [auth A]	1H-INDOLE-3-CARBOXYLIC ACID C9 H7 N O2 KMAKOBLIOCQGJP-UHFFFAOYSA-N
GLV	D [auth A]	GLYOXYLIC ACID C2 H2 O3 HHLFWLYXYJOTON-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.699	α = 90
b = 79.699	β = 90
c = 223.304	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Huang, H.-L., Sacchettini, J.C.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1024055

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary