9BU9 | pdb_00009bu9

Mixed-valent (2/3) dimanganese SfbO

PDB DOI: https://doi.org/10.2210/pdb9BU9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Litorilinea aerophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-16 Released: 2025-08-27
Deposition Author(s): Liu, C., Rittle, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.187 (Depositor), 0.185 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (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

Dimanganese cofactor mediates enzymatic C-H bond hydroxylation

Liu, C., Rittle, J.

To be published.

Macromolecule Content

Total Structure Weight: 171.56 kDa
Atom Count: 12,807
Modeled Residue Count: 1,404
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase family protein	A, B, C, D	372	Litorilinea aerophila	Mutation(s): 0 Gene Names: FKZ61_10105
UniProt
Find proteins for A0A540VG95 (Litorilinea aerophila) Explore A0A540VG95 Go to UniProtKB: A0A540VG95
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A540VG95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	H [auth A], M [auth B], N [auth B], Q [auth C], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	I [auth A] J [auth A] O [auth B] P [auth B] R [auth C] I [auth A], J [auth A], O [auth B], P [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]