7XPC | pdb_00007xpc

Complex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1

PDB DOI: https://doi.org/10.2210/pdb7XPC/pdb

Classification: IMMUNE SYSTEM
Organism(s): Solanum lycopersicum, Phytophthora infestans T30-4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-05-04 Released: 2023-06-07
Deposition Author(s): Hu, Q., Zhou, J., Yao, D., Xing, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free:
0.317 (Depositor), 0.317 (DCC)
R-Value Work:
0.293 (Depositor), 0.292 (DCC)
R-Value Observed:
0.296 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7XPC

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

Literature

Chloroplast Protein GLYK Hijacked by Phytophthora Infestans Effector AVRvnt1 in Cytoplasm to Activate NLR

Hu, Q., Zhou, J., Yao, D., Xing, W.

To be published.

Macromolecule Content

Total Structure Weight: 96.73 kDa
Atom Count: 6,550
Modeled Residue Count: 816
Deposited Residue Count: 842
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glycerate-3-kinase (GLYK)	A, C	337	Solanum lycopersicum	Mutation(s): 6
UniProt
Find proteins for A0A3Q7FWS2 (Solanum lycopersicum) Explore A0A3Q7FWS2 Go to UniProtKB: A0A3Q7FWS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3Q7FWS2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein Avr-vnt11	B, D	84	Phytophthora infestans T30-4	Mutation(s): 0 Gene Names: Avr-vnt1, PITG_16294
UniProt
Find proteins for D0NTY1 (Phytophthora infestans (strain T30-4)) Explore D0NTY1 Go to UniProtKB: D0NTY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0NTY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.317 (Depositor), 0.317 (DCC)
R-Value Work: 0.293 (Depositor), 0.292 (DCC)
R-Value Observed: 0.296 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.285	α = 90
b = 131.285	β = 90
c = 121.968	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-06-07
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Structure summary

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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.