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.

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
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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O22476
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

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

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Entry History

Deposition Data

Released Date: 2016-08-31

Deposition Author(s):

This entry supersedes: 4OA9

Revision History (Full details and data files)

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

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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.