4PQ9 | pdb_00004pq9

Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum

• PDB DOI: https://doi.org/10.2210/pdb4PQ9/pdb

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


• Deposited: 2014-02-28 Released: 2014-03-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum

Dranow, D.M., Davies, D.R., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 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: 58.65 kDa 
• Atom Count: 4,421 
• Modeled Residue Count: 466 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,3-glucanase	A, B	257	Mycobacterium marinum M	Mutation(s): 0  Gene Names: MMAR_2902
UniProt
Find proteins for B2HE62 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HE62  Go to UniProtKB:  B2HE62

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	E [auth A], H [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34PQ9

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.12	α = 109.45
b = 46.84	β = 95.63
c = 51.84	γ = 99.79

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Database references, Structure summary