8FHC | pdb_00008fhc

Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium

PDB DOI: https://doi.org/10.2210/pdb8FHC/pdb

Classification: LYASE
Organism(s): gamma proteobacterium HdN1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-12-13 Released: 2023-12-20
Deposition Author(s): Arenas, R., Wilson, D.K., Mak, W.S., Siegel, J.B.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.236 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.210 (DCC)

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

Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium

Arenas, R., Wilson, D.K., Mak, W.S., Siegel, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 53.49 kDa
Atom Count: 3,729
Modeled Residue Count: 428
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-(MS[2]IO[6]A)-hydroxylase	A, B	223	gamma proteobacterium HdN1	Mutation(s): 0 Gene Names: miaE, HDN1F_16480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHD (Subject of Investigation/LOI) Query on CHD Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
BR (Subject of Investigation/LOI) Query on BR 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 H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], K [auth B], L [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]