8XP6 | pdb_00008xp6

2OG-Fe(II) oxygenase-ColD

PDB DOI: https://doi.org/10.2210/pdb8XP6/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces collinus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-01-03 Released: 2025-01-15
Deposition Author(s): Zhang, B., Shi, J., Zhang, Y., Ge, H.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.174 (Depositor), 0.175 (DCC)
R-Value Work:
0.159 (Depositor), 0.163 (DCC)
R-Value Observed:
0.160 (Depositor)

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

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This is version 1.1 of the entry. See complete history.

Literature

Biosynthesis of Collinodin Unveils Iterative Oxidative and Prenylation Modifications

Shi, J., Zhang, Y., Ren, W.Q., Shi, Y., Wei, Y.Y., Zhang, B., Jiao, R.H., Ge, H.M.

(2025) ACS Catal 15: 6628-6639

DOI: https://doi.org/10.1021/acscatal.5c01005

Macromolecule Content

Total Structure Weight: 34.89 kDa
Atom Count: 2,839
Modeled Residue Count: 294
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2OG-Fe(II) oxygenase	A	312	Streptomyces collinus	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAK2 (Streptomyces sp. yr375) Explore A0ACD6BAK2 Go to UniProtKB: A0ACD6BAK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAK2
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: 1.40 Å
R-Value Free: 0.174 (Depositor), 0.175 (DCC)
R-Value Work: 0.159 (Depositor), 0.163 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.55	α = 90
b = 62.75	β = 90
c = 92.14	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81925033, 22193071, 81991522, 81991524, 22107048, and 22377052
Ministry of Science and Technology (MoST, China)	China	2022YFC2804100, 2022YFC2303100, and 2018YFA0902000

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2025-07-30
Changes: Database references

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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.