8YXT

Crystal structure of PtmB

PDB DOI: https://doi.org/10.2210/pdb8YXT/pdb

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

Deposited: 2024-04-02 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.261
R-Value Work: 0.227

Starting Model: in silico
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Ligand Structure Quality Assessment

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

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

Macromolecule Content

Total Structure Weight: 45.92 kDa
Atom Count: 3,005
Modelled Residue Count: 380
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PtmB	A	412	Kitasatospora mediocidica KCTC 9733	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.261
R-Value Work: 0.227
Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.712	α = 90
b = 88.712	β = 90
c = 139.892	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-11-20
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.