8FHB | pdb_00008fhb

Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.

PDB DOI: https://doi.org/10.2210/pdb8FHB/pdb

Classification: LYASE
Organism(s): Synechococcus sp. RCC307
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: 1.95 Å
R-Value Free:
0.217 (Depositor), 0.221 (DCC)
R-Value Work:
0.169 (Depositor), 0.181 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8FHB

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

Literature

Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.

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

To be published.

Macromolecule Content

Total Structure Weight: 25.84 kDa
Atom Count: 1,700
Modeled Residue Count: 204
Deposited Residue Count: 229
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-(MS[2]IO[6]A)-hydroxylase	A	229	Synechococcus sp. RCC307	Mutation(s): 0 Gene Names: miaE
UniProt
Find proteins for A0ACD6B9G8 (Synechococcus sp. (strain RCC307)) Explore A0ACD6B9G8 Go to UniProtKB: A0ACD6B9G8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9G8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.217 (Depositor), 0.221 (DCC)
R-Value Work: 0.169 (Depositor), 0.181 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.192	α = 90
b = 74.33	β = 90
c = 111.953	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release

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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.