9THS | pdb_00009ths

Room temperature structure of Ascorbate Peroxidase at 1.54A

PDB DOI: https://doi.org/10.2210/pdb9THS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Glycine max
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-03 Released: 2025-12-17
Deposition Author(s): Udiniya, M., Moody, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.201 (Depositor), 0.205 (DCC)
R-Value Work:
0.167 (Depositor), 0.173 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Room temperature structure of Ascorbate Peroxidase at 1.54A

Udiniya, M., Moody, P.

To be published.

Macromolecule Content

Total Structure Weight: 27.61 kDa
Atom Count: 2,058
Modeled Residue Count: 249
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ascorbate peroxidase	A	249	Glycine max	Mutation(s): 0 Gene Names: apx1, GLYMA_U021900 EC: 1.11.1.11
UniProt
Find proteins for Q43758 (Glycine max) Explore Q43758 Go to UniProtKB: Q43758
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q43758
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.201 (Depositor), 0.205 (DCC)
R-Value Work: 0.167 (Depositor), 0.173 (DCC)

Diffraction Data:

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.831	α = 90
b = 82.831	β = 90
c = 76.017	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
CrysalisPro	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: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release
Version 1.1: 2026-02-11
Changes: Database references, Experimental preparation

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