8Q6X

Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae

PDB DOI: https://doi.org/10.2210/pdb8Q6X/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 ?
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (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: 91.38 kDa
Atom Count: 6,490
Modelled Residue Count: 777
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B	410	Streptomyces katrae	Mutation(s): 0 Gene Names: VR44_17910
UniProt
Find proteins for A0A0F4JF04 (Streptomyces katrae) Explore A0A0F4JF04 Go to UniProtKB: A0A0F4JF04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F4JF04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 ?
R-Value Free: 0.208 (Depositor), 0.210 (DCC)
R-Value Work: 0.170 (Depositor), 0.180 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 63.166	α = 90
b = 95.544	β = 109.22
c = 81.459	γ = 90

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.