8WM2 | pdb_00008wm2

Crystal structure of AbmM

PDB DOI: https://doi.org/10.2210/pdb8WM2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces sp. ATCC 700974
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-02 Released: 2024-10-09
Deposition Author(s): Ushimaru, R., Mori, T., Abe, I., Liu, H.-w.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8WM2

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

Literature

Crystal structure of AbmM

Ushimaru, R., Mori, T., Abe, I., Liu, H.-w.

To be published.

Macromolecule Content

Total Structure Weight: 73.75 kDa
Atom Count: 4,666
Modeled Residue Count: 591
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-S radical SAM	A, B	325	Streptomyces sp. ATCC 700974	Mutation(s): 0
UniProt
Find proteins for I1ZAZ9 (Streptomyces sp. ATCC 700974) Explore I1ZAZ9 Go to UniProtKB: I1ZAZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I1ZAZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] 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 J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [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 J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [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 J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.79	α = 90
b = 81.026	β = 90
c = 131.842	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

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