5LPV | pdb_00005lpv

Crystal structure of the BRI1 kinase domain (865-1160) in complex with AMPPNP and Mn from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb5LPV/pdb
• Entry: 5LPV supersedes: 4OA9

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-15 Released: 2016-08-31 
• Deposition Author(s): Bojar, D., Martinez, J., Hothorn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.233 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation.

Bojar, D., Martinez, J., Santiago, J., Rybin, V., Bayliss, R., Hothorn, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.98 kDa 
• Atom Count: 2,161 
• Modeled Residue Count: 285 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A	296	Arabidopsis thaliana	Mutation(s): 1  Gene Names: BRI1, At4g39400, F23K16.30 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for O22476 (Arabidopsis thaliana) Explore O22476  Go to UniProtKB:  O22476

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
TPO	A	THR	Phosphorylation	C4 H10 N O6 P
SEP	A	SER	Phosphorylation	C3 H8 N O6 P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.233 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.63	α = 90
b = 115.63	β = 90
c = 49.64	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Bojar, D., Martinez, J., Hothorn, M.
• This entry supersedes: 4OA9

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary