5IR2 | pdb_00005ir2

Crystal structure of novel cellulases from microbes associated with the gut ecosystem

• PDB DOI: https://doi.org/10.2210/pdb5IR2/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides johnsonii DSM 18315
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-03-11 Released: 2016-03-23 
• Deposition Author(s): Chang, C., Mack, J., Jedrzejczak, R., 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: 2.08 Å
• R-Value Free: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structure of novel cellulases from microbes associated with the gut ecosystem

Chang, C., Mack, J., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.23 kDa 
• Atom Count: 2,045 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase	A	222	Parabacteroides johnsonii DSM 18315	Mutation(s): 1  Gene Names: PRABACTJOHN_04122
UniProt
Find proteins for B7BGD3 (Parabacteroides johnsonii DSM 18315) Explore B7BGD3  Go to UniProtKB:  B7BGD3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SRT	C [auth A]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.24	α = 90
b = 100.24	β = 90
c = 129.698	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Chang, C., Mack, J., Jedrzejczak, R., 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	GM115586

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary