8Q6Z | pdb_00008q6z

Crystal structure of Cytochrome P450 GymB1 from Streptomyces flavidovirens

PDB DOI: https://doi.org/10.2210/pdb8Q6Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces flavidovirens DSM 40150
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-06-26
Deposition Author(s): Freytag, J., Kelm, T., Stehle, T., Zocher, G.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.214 (Depositor), 0.219 (DCC)
R-Value Work:
0.185 (Depositor), 0.191 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Intramolecular Coupling and Nucleobase Transfer - How Cytochrome P450 Enzymes GymBx Establish Their Chemoselectivity

Freytag, J., Martin, A., Muller, J.C., Kelm, T., Stehle, T., Li, S.M., Zocher, G.

(2024) ChemCatChem 16

DOI: https://doi.org/10.1002/cctc.202481002

Macromolecule Content

Total Structure Weight: 43.96 kDa
Atom Count: 3,288
Modeled Residue Count: 390
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GymB1	A	395	Streptomyces flavidovirens DSM 40150	Mutation(s): 0
UniProt
Find proteins for A0AAT8XUD6 (Streptomyces flavidovirens DSM 40150) Explore A0AAT8XUD6 Go to UniProtKB: A0AAT8XUD6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAT8XUD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.214 (Depositor), 0.219 (DCC)
R-Value Work: 0.185 (Depositor), 0.191 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.076	α = 90
b = 98.076	β = 90
c = 94.28	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	TRR261

Revision History (Full details and data files)

Version 1.0: 2024-06-26
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.