6JT6

Crystal structure of cytochrome b domain of Pyranose Dehydrogenase from Coprinopsis cinerea

• PDB DOI: https://doi.org/10.2210/pdb6JT6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Coprinopsis cinerea
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-04-09 Released: 2019-11-13 
• Deposition Author(s): Takeda, K., Ishida, T., Yoshida, M., Samejima, M., Ohno, H., Igarashi, K., Nakamura, N.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.26 kDa 
• Atom Count: 1,716 
• Modelled Residue Count: 195 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular PQQ-dependent sugar dehydrogenase	A	197	Coprinopsis cinerea	Mutation(s): 0  Gene Names: CcSDH
UniProt
Find proteins for A8P0V4 (Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003)) Explore A8P0V4  Go to UniProtKB:  A8P0V4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.138	α = 90
b = 59.741	β = 90.68
c = 40.858	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Takeda, K., Ishida, T., Yoshida, M., Samejima, M., Ohno, H., Igarashi, K., Nakamura, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K17703

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Structure summary
• Version 1.2: 2019-12-11
  Changes: Database references
• Version 1.3: 2020-04-15
  Changes: Data collection, Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary