9EPG | pdb_00009epg

DtpAa Y389F 24 fs 10 microjoules XFEL Pulse Data Collection

PDB DOI: https://doi.org/10.2210/pdb9EPG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lividans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-03-18 Released: 2025-03-26
Deposition Author(s): Williams, L.J., Owen, R.L., Worrall, J.A.R., Hough, M.A.
Funding Organization(s): Diamond Light Source

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 ?
R-Value Free:
0.169 (Depositor), 0.169 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DtpAa Y389F 24 fs 10 microjoules XFEL Pulse Data Collection

Williams, L.J., Owen, R.L., Worrall, J.A.R., Hough, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 81.71 kDa
Atom Count: 6,234
Modelled Residue Count: 725
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase	A, B	373	Streptomyces lividans	Mutation(s): 1 Gene Names: SLI_2602 EC: 1.11.1
UniProt
Find proteins for A0A7U9DT46 (Streptomyces lividans 1326) Explore A0A7U9DT46 Go to UniProtKB: A0A7U9DT46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7U9DT46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) 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: 1.33 ?
R-Value Free: 0.169 (Depositor), 0.169 (DCC)
R-Value Work: 0.153 (Depositor), 0.153 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 72.72	α = 90
b = 68.2	β = 105.6
c = 74.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data scaling
REFMAC	phasing
Coot	model building
CrystFEL	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Worrall, J.A.R.

Funding Organization	Location	Grant Number
Diamond Light Source	United Kingdom	STU0436

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.