3RXZ | pdb_00003rxz

Crystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb3RXZ/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-05-10 Released: 2011-06-22 
• Deposition Author(s): Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.211 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis

Michalska, K., Tesar, C., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 134.06 kDa 
• Atom Count: 9,319 
• Modeled Residue Count: 1,146 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polysaccharide deacetylase	A, B, C, D	300	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_4373
UniProt
Find proteins for A0R0G0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R0G0  Go to UniProtKB:  A0R0G0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], G [auth B], I [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.211 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33RXZ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.212	α = 90
b = 59.592	β = 95.35
c = 130.387	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
SHELXD	phasing
SHELXE	model building
RESOLVE	model building
DM	model building
ARP/wARP	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary