9EPD | pdb_00009epd

DtpAa Y389F 8 fs 10 microjoules XFEL Pulse Data Collection

PDB DOI: https://doi.org/10.2210/pdb9EPD/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: 1.48 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.187 (DCC)
R-Value Observed:
0.179 (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

DtpAa Y389F 8 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: 6,205
Modelled Residue Count: 724
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

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(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: 1.48 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor), 0.187 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

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

Software Package:

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