6AXE | pdb_00006axe

Crystal structure of a malate synthase G from Mycobacterium marinum bound to acetyl CoA

• PDB DOI: https://doi.org/10.2210/pdb6AXE/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium marinum M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-06 Released: 2017-09-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a malate synthase G from Mycobacterium marinum bound to acetyl CoA

Edwards, T.E., Dranow, D.M., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.98 kDa 
• Atom Count: 13,195 
• Modeled Residue Count: 1,453 
• Deposited Residue Count: 1,478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate synthase G	A, B	739	Mycobacterium marinum M	Mutation(s): 0  Gene Names: glcB, MMAR_2713 EC: 2.3.3.9
UniProt
Find proteins for B2HSY2 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HSY2  Go to UniProtKB:  B2HSY2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	C [auth A], F [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36AXE

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.6	α = 90
b = 86.98	β = 98.45
c = 124.13	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description