5GYY | pdb_00005gyy

Plant receptor complex

PDB DOI: https://doi.org/10.2210/pdb5GYY/pdb

Classification: PLANT PROTEIN
Organism(s): Brassica rapa
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-09-24 Released: 2017-09-27
Deposition Author(s): Ma, R., Han, Z., Hu, Z., Lin, G., Gong, X., Zhang, H., June, N., Chai, J.
Funding Organization(s): National Science Foundation of China, Chinese Ministry of Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.196 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Plant receptor complex at 2.35 Angstroms resolution

Ma, R., Han, Z., Hu, Z., Lin, G., Gong, X., Zhang, H., June, N., Chai, J.

To be published.

Macromolecule Content

Total Structure Weight: 105.1 kDa
Atom Count: 7,701
Modeled Residue Count: 917
Deposited Residue Count: 928
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-receptor kinase SRK9	A, B	405	Brassica rapa	Mutation(s): 0 EC: 2.7.11.1
UniProt
Find proteins for Q7DN95 (Brassica campestris) Explore Q7DN95 Go to UniProtKB: Q7DN95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7DN95
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-locus protein 11	C [auth G], D [auth H]	59	Brassica rapa	Mutation(s): 0 Gene Names: SP11
UniProt
Find proteins for Q9ST12 (Brassica campestris) Explore Q9ST12 Go to UniProtKB: Q9ST12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ST12
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth G] Focus chain D [auth H]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain F [auth H] MOL2 format, chain E [auth G] MOL2 format, chain F [auth H] mmCIF format, chain E [auth G] mmCIF format, chain F [auth H]	E [auth G], F [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth G] Focus chain F [auth H] Interactions & Density Focus chain E [auth G] Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.196 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.249	α = 90
b = 135.121	β = 90
c = 153.907	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation of China	China	31130063
Chinese Ministry of Science and Technology	China	2015CB910200

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary