8W6Z

Substrate-bound crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins

• PDB DOI: https://doi.org/10.2210/pdb8W6Z/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp.
• Mutation(s): No 


• Deposited: 2023-08-30 Released: 2024-06-12 
• Deposition Author(s): Fang, C., Zhang, L., Zhu, Y., Zhang, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Substrate-bound crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins

Fang, C., Zhang, L., Zhu, Y., Zhang, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 48.99 kDa 
• Atom Count: 3,384 
• Modelled Residue Count: 406 
• Deposited Residue Count: 438 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	428	Streptomyces sp.	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-D4P-GLU-GLY-BB8-PRO-KJW-GLY-A1D5P-DPN	B	10	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
R8L (Subject of Investigation/LOI)	D [auth B]	(E)-3-[2-[(2R,3S)-3-[(1R)-1-aminocarbonyloxypropyl]oxiran-2-yl]phenyl]prop-2-enoic acid C15 H17 N O5 APIHDLCQFHISLU-PQPVHHHVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1D5P	B	D-PEPTIDE LINKING	C9 H11 N O4		TYR
BB8	B	L-PEPTIDE LINKING	C9 H11 N O3		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002429	B	cihanmycin G	Cyclic peptide / Unknown

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.082	α = 90
b = 100.162	β = 90
c = 105.811	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
MOLREP	phasing
CrysalisPro	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Fang, C., Zhang, L., Zhu, Y., Zhang, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177118
National Natural Science Foundation of China (NSFC)	China	31820103003
National Natural Science Foundation of China (NSFC)	China	31630004

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 2.0: 2024-06-19
  Changes: Atomic model, Data collection, Derived calculations, Structure summary