6W0P | pdb_00006w0p

Putative kojibiose phosphorylase from human microbiome

• PDB DOI: https://doi.org/10.2210/pdb6W0P/pdb

• Classification: LIGASE
• Organism(s): gut metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-02 Released: 2020-03-18 
• Deposition Author(s): Dementiev, A., Osipiuk, J., Endres, M., Wakatsuki, S., Hess, M., Joachimiak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.246 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Putative kojibiose phosphorylase from human microbiome

Dementiev, A., Osipiuk, J., Endres, M., Wakatsuki, S., Hess, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 356.28 kDa 
• Atom Count: 25,131 
• Modeled Residue Count: 2,899 
• Deposited Residue Count: 3,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kojibiose phosphorylase	A, B, C, D	760	gut metagenome	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.246 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.215	α = 90
b = 200.451	β = 90
c = 293.122	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Dementiev, A., Osipiuk, J., Endres, M., Wakatsuki, S., Hess, M., Joachimiak, A.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description