9YL8 | pdb_00009yl8

Crystal structure of Ni(II)-bound SeMet-HrmI from Streptomyces griseoflavus

PDB DOI: https://doi.org/10.2210/pdb9YL8/pdb

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

Deposited: 2025-10-08 Released: 2026-10-21
Deposition Author(s): Pope, S.R., Boal, A.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.189 (Depositor), 0.188 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9YL8

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

Literature

Interconverting Peroxodiiron Intermediates and Capture of Substrate by a Protonated Species in the Oxidation of L-Lysine to 6-Nitro-L-Norleucine by HrmI from the Hormaomycin Pathway

Pope, S.R., Nair, M.A., Boal, A.K., Krebs, C., Bollinger, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 38.95 kDa
Atom Count: 2,934
Modeled Residue Count: 343
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HrmI	A	343	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
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.189 (Depositor), 0.188 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.129	α = 90
b = 93.129	β = 90
c = 85.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	500000015890

Revision History (Full details and data files)

Version 1.0: 2026-10-21
Type: Initial release