8Q6Z

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), 0.220 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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
Modelled Residue Count: 390
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GymB1	A	395	Streptomyces flavidovirens DSM 40150	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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), 0.220 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (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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Ligand Structure Quality Assessment

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

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.