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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.215 (Depositor), 0.221 (DCC)
R-Value Work:
0.180 (Depositor), 0.191 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium

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

To be published.

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

Find similar proteins by:

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	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.215 (Depositor), 0.221 (DCC)
R-Value Work: 0.180 (Depositor), 0.191 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.