5CSU

Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak

PDB DOI: https://doi.org/10.2210/pdb5CSU/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-23 Released: 2015-11-04
Deposition Author(s): O'Neill, E.C., Stevenson, C.E.M., Tantanarat, K., Latousakis, D., Donaldson, M.I., Rejzek, M., Limpaseni, T., Smith, A.M., Field, R.A., Lawson, D.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.249
R-Value Work: 0.207
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 129.16 kDa
Atom Count: 8,356
Modelled Residue Count: 1,036
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic	A, B	564	Arabidopsis thaliana	Mutation(s): 0 Gene Names: DPE1, At5g64860, MXK3.9 EC: 2.4.1.25
UniProt
Find proteins for Q9LV91 (Arabidopsis thaliana) Explore Q9LV91 Go to UniProtKB: Q9LV91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LV91
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, E	2		N/A	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G90989WB GlyCosmos: G90989WB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D, F	3		N/A	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G21221NT GlyCosmos: G21221NT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HMC Query on HMC Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	I [auth A], J [auth A], L [auth B], M [auth B]	5-HYDROXYMETHYL-CHONDURITOL C₇ H₁₂ O₅ PJPGMULJEYSZBS-VZFHVOOUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B]	G [auth A], H [auth A], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.249
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.83	α = 64.59
b = 74.13	β = 69.76
c = 79.73	γ = 66.57

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J004561/1

Revision History (Full details and data files)

Version 1.0: 2015-11-04
Type: Initial release
Version 1.1: 2015-12-23
Changes: Database references
Version 1.2: 2017-08-30
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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5CSU

Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources