5JMB | pdb_00005jmb

The Crystal structure of the N-terminal domain of a novel cellulases from Bacteroides coprocola

• PDB DOI: https://doi.org/10.2210/pdb5JMB/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola coprocola
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-28 Released: 2016-06-29 
• Deposition Author(s): Tan, K., Gu, M., Jedrzejczak, R., Joachimiak, A.
• 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: 2.05 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

The Crystal structure of the N-terminal domain of a novel cellulases from Bacteroides coprocola (CASP target)

Tan, K., Gu, M., Jedrzejczak, R., 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)

Macromolecule Content 

• Total Structure Weight: 21.16 kDa 
• Atom Count: 1,505 
• Modeled Residue Count: 182 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	94	Phocaeicola coprocola	Mutation(s): 0
UniProt
Find proteins for B3JI28 (Phocaeicola coprocola DSM 17136) Explore B3JI28  Go to UniProtKB:  B3JI28

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.86	α = 90
b = 47.86	β = 90
c = 292.85	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Tan, K., Gu, M., Jedrzejczak, R., Joachimiak, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	115586

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary