8E8W | pdb_00008e8w

Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 mononuclear Fe(II) structure on the HDO cofactor assembly pathway

PDB DOI: https://doi.org/10.2210/pdb8E8W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces achromogenes subsp. streptozoticus
Expression System: Streptomyces achromogenes subsp. streptozoticus
Mutation(s): No

Deposited: 2022-08-25 Released: 2023-08-30
Deposition Author(s): McBride, M.J., 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: 2.50 Å
R-Value Free:
0.302 (Depositor), 0.310 (DCC)
R-Value Work:
0.246 (Depositor), 0.253 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 mononuclear Fe(II) structure on the HDO cofactor assembly pathway

McBride, M.J., Boal, A.K., Bollinger Jr., J.M.

To be published.

Macromolecule Content

Total Structure Weight: 112.31 kDa
Atom Count: 7,590
Modeled Residue Count: 905
Deposited Residue Count: 982
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin domain-containing diiron protein	A, B	491	Streptomyces achromogenes subsp. streptozoticus	Mutation(s): 0 Gene Names: stzF, sznF EC: 1.14.13.250
UniProt
Find proteins for A0A411MR89 (Streptomyces achromogenes subsp. streptozoticus) Explore A0A411MR89 Go to UniProtKB: A0A411MR89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A411MR89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.302 (Depositor), 0.310 (DCC)
R-Value Work: 0.246 (Depositor), 0.253 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.73	α = 90
b = 106.368	β = 90
c = 150.41	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.