9SBE | pdb_00009sbe

Crystal structure of Amborella trichopoda ACCO2 mutant - Y163F in complex with Fe and ACC

PDB DOI: https://doi.org/10.2210/pdb9SBE/pdb

Classification: PLANT PROTEIN
Organism(s): Amborella trichopoda
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-08 Released: 2026-08-19
Deposition Author(s): Sun, Y., Dhingra, S., Allen, M.D., Zhang, Z., Brewitz, L., Schofield, C.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Amborella trichopoda ACCO2 mutant - Y163F in complex with Fe and ACC

Sun, Y., Dhingra, S., Allen, M.D., Zhang, Z., Brewitz, L., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 35.97 kDa
Atom Count: 2,626
Modeled Residue Count: 305
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aminocyclopropanecarboxylate oxidase	A	314	Amborella trichopoda	Mutation(s): 0 Gene Names: AMTR_s00112p00098670 EC: 1.14.17.4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1AC (Subject of Investigation/LOI) Query on 1AC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-AMINOCYCLOPROPANECARBOXYLIC ACID C₄ H₇ N O₂ PAJPWUMXBYXFCZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CO (Subject of Investigation/LOI) Query on CO 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]	COBALT (II) ION Co XLJKHNWPARRRJB-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: 1.75 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.078	α = 90
b = 56.257	β = 90
c = 113.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Schofield, C.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V003291/1

Revision History (Full details and data files)

Version 1.0: 2026-08-19
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.