9WTU | pdb_00009wtu

Crystal structure of HrmI in complex with the diferrous iron and lysine

PDB DOI: https://doi.org/10.2210/pdb9WTU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces griseoflavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-17 Released: 2026-09-23
Deposition Author(s): Deng, Z.W., Rao, Y.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.189 (Depositor), 0.199 (DCC)
R-Value Work:
0.153 (Depositor), 0.166 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9WTU

Ligand Structure Quality Assessment

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

Literature

Structural and mechanistic investigation on the release and recruiting of iron within the catalytic cycle of HrmI.

Deng, Z.W., Rao, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 40.55 kDa
Atom Count: 3,061
Modeled Residue Count: 341
Deposited Residue Count: 357
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HrmI	A	357	Streptomyces griseoflavus	Mutation(s): 0
UniProt
Find proteins for F8S6W0 (Streptomyces griseoflavus) Explore F8S6W0 Go to UniProtKB: F8S6W0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8S6W0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.189 (Depositor), 0.199 (DCC)
R-Value Work: 0.153 (Depositor), 0.166 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.75	α = 90
b = 112.75	β = 90
c = 68.487	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	2021YFC2102700
Other private	China	BK20202002
Other private	China	KYCX20_1812
Other private	China	KYCX20_1816

Revision History (Full details and data files)

Version 1.0: 2026-09-23
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.