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- PDB-5lpz: Crystal structure of the BRI1 kinase domain (865-1196) in complex... -

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Basic information

Entry
Database: PDB / ID: 5lpz
TitleCrystal structure of the BRI1 kinase domain (865-1196) in complex with ADP from Arabidopsis thaliana
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsTRANSFERASE / brassinosteroid receptor / kinase domain / dual-specificify kinase / membrane receptor kinase / plasma membrane
Function / homology
Function and homology information


detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / response to UV-B / steroid binding ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / endosome membrane / non-specific serine/threonine protein kinase / protein kinase activity / endosome / protein heterodimerization activity / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBojar, D. / Martinez, J. / Hothorn, M.
CitationJournal: Plant J. / Year: 2014
Title: Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation.
Authors: Bojar, D. / Martinez, J. / Santiago, J. / Rybin, V. / Bayliss, R. / Hothorn, M.
History
DepositionAug 15, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionAug 24, 2016ID: 4OA2
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein BRASSINOSTEROID INSENSITIVE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5892
Polymers37,1611
Non-polymers4271
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-5 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.833, 116.833, 50.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Protein BRASSINOSTEROID INSENSITIVE 1 / AtBRI1 / Brassinosteroid LRR receptor kinase


Mass: 37161.430 Da / Num. of mol.: 1 / Fragment: UNP residues 865-1196 / Mutation: T872A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRI1, At4g39400, F23K16.30 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 37.5% MPD/PEG 1000/PEG 3350 morpheus mix, 0.1 M amino acids mix, 0.1 M MOPS/Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91838 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 2.48→19.47 Å / Num. obs: 14064 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 20.02 % / Biso Wilson estimate: 67.34 Å2 / CC1/2: 1 / Rsym value: 0.097 / Net I/σ(I): 22.43
Reflection shellResolution: 2.48→2.62 Å / Redundancy: 18.66 % / Mean I/σ(I) obs: 2.63 / CC1/2: 0.794 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UIM

3uim


Resolution: 2.48→19.47 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.56 / Phase error: 30.35
RfactorNum. reflection% reflection
Rfree0.2529 1310 4.83 %
Rwork0.224 --
obs0.2255 14055 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.48→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 27 19 2216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022246
X-RAY DIFFRACTIONf_angle_d0.583049
X-RAY DIFFRACTIONf_dihedral_angle_d10.7211339
X-RAY DIFFRACTIONf_chiral_restr0.038344
X-RAY DIFFRACTIONf_plane_restr0.003382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4765-2.57550.33691340.33942610X-RAY DIFFRACTION89
2.5755-2.69240.32751800.30852852X-RAY DIFFRACTION100
2.6924-2.8340.29261330.32924X-RAY DIFFRACTION100
2.834-3.01090.3531630.2972876X-RAY DIFFRACTION100
3.0109-3.24240.28231250.2762945X-RAY DIFFRACTION100
3.2424-3.56690.32221290.25922905X-RAY DIFFRACTION100
3.5669-4.07890.2771530.21752897X-RAY DIFFRACTION100
4.0789-5.12340.19561560.1782890X-RAY DIFFRACTION100
5.1234-19.47280.20481370.18352912X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.7845-3.7872-4.71276.39465.29055.8570.4978-0.4810.7639-0.3410.2264-0.0965-0.62360.2751-0.26460.45450.04760.05120.4915-0.02270.63630.939935.661417.468
27.8515-1.4027-1.22156.90680.06563.8139-0.3003-0.3794-0.62390.3970.3263-0.309-0.02680.2453-0.02840.56050.1212-0.02570.3827-0.06260.653342.983320.517815.3933
32.9802-0.743-0.13985.2935-0.83226.4395-0.4812-1.9806-1.8871.9472-0.4584-1.6794-0.05592.70660.68011.39770.1459-0.30151.41860.44341.472852.875610.017830.0503
45.80431.7137-0.00127.6284.39582.85861.0304-0.2643-0.37580.0054-0.80861.06712.42531.1251-0.1071.76730.3010.08781.19110.53521.684941.83962.475735.6353
53.60252.25961.80595.5881-0.21533.3483-0.8693-0.7747-2.35241.15880.6296-0.28780.61440.16410.07320.91520.26230.12470.54730.09251.379845.97996.501115.5857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 866:969)
2X-RAY DIFFRACTION2(chain A and resseq 970:1086)
3X-RAY DIFFRACTION3(chain A and resseq 1095:1116)
4X-RAY DIFFRACTION4(chain A and resseq 1117:1124)
5X-RAY DIFFRACTION5(chain A and resseq 1126:1160)

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