8YY7

Crystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and Hypoxanthine

• PDB DOI: https://doi.org/10.2210/pdb8YY7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Kitasatospora mediocidica KCTC 9733
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-03 Released: 2024-11-20 
• Deposition Author(s): Zhang, Z.Y., Qu, X.D., Duan, B.R., Wei, G.Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.195 

Starting Model: in silico

Literature

A nucleobase-driven P450 peroxidase system enables regio- and stereo-specific formation of C─C and C─N bonds

Wei, G.Z., Duan, B.R., Zhou, T.P., Tian, W., Sun, C., Lin, Z., Deng, Z., Wang, B., Zhang, Z.Y., Qu, X.D.

(2024) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.2412890121

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 92.85 kDa 
• Atom Count: 6,811 
• Modelled Residue Count: 776 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PtmB	A, B	412	Kitasatospora mediocidica KCTC 9733	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
UYM	C [auth A], F [auth B]	(3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione C22 H20 N4 O2 DNHODRZUCGXYKU-PMACEKPBSA-N
HPA	D [auth A], G [auth B]	HYPOXANTHINE C5 H4 N4 O FDGQSTZJBFJUBT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.195 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.97	α = 90
b = 84.97	β = 90
c = 136.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Zhang, Z.Y., Qu, X.D., Duan, B.R., Wei, G.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800052

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release