8X38 | pdb_00008x38

Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium

• PDB DOI: https://doi.org/10.2210/pdb8X38/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phanerochaete chrysosporium RP-78
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-12 Released: 2024-01-24 
• Deposition Author(s): Suzuki, H., Mori, R., Ishida, T., Igarashi, K., Shimizu, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: in silico

Literature

Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium

Mori, R., Suzuki, H., Ishida, T., Igarashi, K., Kato, M., Shimizu, M.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.66 kDa 
• Atom Count: 3,564 
• Modeled Residue Count: 430 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarboxylative Vanillate 1-Hydroxylase	A	496	Phanerochaete chrysosporium RP-78	Mutation(s): 0  Gene Names: fgenesh1_kg.3_#_10694_#_transcript/44524 EC: 1.14.13.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ACT	C [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:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.632	α = 90
b = 97.13	β = 90
c = 106.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Suzuki, H., Mori, R., Ishida, T., Igarashi, K., Shimizu, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K05815

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release