8HYG | pdb_00008hyg

Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6

PDB DOI: https://doi.org/10.2210/pdb8HYG/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-06 Released: 2023-01-25
Deposition Author(s): Tsao, H.E., Lui, S.N., Wong, K.B.
Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.169 (Depositor), 0.168 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6

Tsao, H.E., Lui, S.N., Wong, K.B.

To be published.

Macromolecule Content

Total Structure Weight: 18.87 kDa
Atom Count: 1,223
Modeled Residue Count: 147
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar-sorting receptor 1	A	165	Arabidopsis thaliana	Mutation(s): 0 Gene Names: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20
UniProt
Find proteins for P93026 (Arabidopsis thaliana) Explore P93026 Go to UniProtKB: P93026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P93026
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A], G [auth A], H [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain B [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain B [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain B [auth A]	B [auth A], I [auth A], J [auth A], K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain B [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.169 (Depositor), 0.168 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.987	α = 90
b = 60.318	β = 103.36
c = 38.466	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Tsao, H.E.

Lui, S.N.

Wong, K.B.

Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	CUHK14151416
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	C4041-18EF
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	AoE/M-05/12
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	AoE/M403/16
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	C4033-19E