4YYF | pdb_00004yyf

The crystal structure of a glycosyl hydrolase of GH3 family member from [Mycobacterium smegmatis str. MC2 155

• PDB DOI: https://doi.org/10.2210/pdb4YYF/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-23 Released: 2015-04-08 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

The crystal structure of a glycosyl hydrolase of GH3 family member from [Mycobacterium smegmatis str. MC2 155

Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 112.93 kDa 
• Atom Count: 7,645 
• Modeled Residue Count: 981 
• Deposited Residue Count: 1,095 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B, C	365	Mycolicibacterium smegmatis MC2 155	Mutation(s): 1  Gene Names: MSMEG_0361, MSMEI_0354, LJ00_01805 EC: 3.2.1.52
UniProt
Find proteins for A0QPD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPD6  Go to UniProtKB:  A0QPD6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], I [auth B], J [auth B], K [auth B], N [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	F [auth A], L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.067	α = 90
b = 130.941	β = 90
c = 85.986	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary