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- PDB-5lpy: Crystal structure of the BRI1 kinase domain (865-1160) in complex... -

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Basic information

Entry
Database: PDB / ID: 5lpy
TitleCrystal structure of the BRI1 kinase domain (865-1160) in complex with ATP 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 / positive regulation of flower development / seedling 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 / positive regulation of flower development / seedling development / brassinosteroid mediated signaling pathway / leaf development / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / non-specific serine/threonine protein kinase / protein kinase activity / endosome / endosome membrane / 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'-TRIPHOSPHATE / Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBojar, D. / Martinez, J. / Hothorn, M.
Citation
Journal: to be published
Title: Crystal structure of the BRI1 kinase domain (865-1160) in complex with ATP from Arabidopsis thaliana
Authors: Bojar, D. / Martinez, J. / Hothorn, M.
#1: Journal: 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: 4OAB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 23, 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)33,9492
Polymers33,4421
Non-polymers5071
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.823, 115.823, 49.898
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: 33442.203 Da / Num. of mol.: 1 / 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 (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): RIL
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 20K/MME 550 morpheus mix, 0.12 M eth glycol mix, 0.1 M Hepes pH 7.5 soaked with 30 mM ATP in xtal condition (around 3 min)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.3→44.67 Å / Num. obs: 17194 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 71.46 Å2 / CC1/2: 1 / Rsym value: 0.043 / Net I/σ(I): 36.77
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 2.49 / CC1/2: 0.767 / % possible all: 98.8

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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: 2.3→44.67 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.11
RfactorNum. reflection% reflection
Rfree0.248 877 5.1 %
Rwork0.2008 --
obs0.2031 17190 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 31 10 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052261
X-RAY DIFFRACTIONf_angle_d0.7143072
X-RAY DIFFRACTIONf_dihedral_angle_d12.6141338
X-RAY DIFFRACTIONf_chiral_restr0.043342
X-RAY DIFFRACTIONf_plane_restr0.003384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.44440.34141520.26882662X-RAY DIFFRACTION99
2.4444-2.63310.30821640.24382705X-RAY DIFFRACTION100
2.6331-2.8980.26011460.2242682X-RAY DIFFRACTION100
2.898-3.31730.29661260.21712749X-RAY DIFFRACTION100
3.3173-4.17890.24291460.19692709X-RAY DIFFRACTION100
4.1789-44.68380.22261430.18552806X-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)
14.9522-3.0598-2.16757.99782.64034.25860.1566-0.1650.6379-0.40750.16990.0182-0.27050.219-0.25630.48270.06110.01050.6369-0.00250.632330.732835.490717.5929
28.1918-0.1948-1.6456.9758-0.04024.8012-0.2037-0.302-0.2030.14710.2968-0.1688-0.23340.1611-0.10130.59770.0813-0.00540.3715-0.03260.487542.532520.428415.2049
36.00364.0662-4.70554.54910.07249.58560.0486-2.2659-1.61411.5087-0.0368-0.9752-0.64481.2440.20641.29890.1638-0.32351.41260.41160.877552.650410.373829.9518
42.82412.39621.33454.4682.06318.46730.3267-1.286-1.03450.2421-0.5842-0.56491.4961.330.40451.28580.1425-0.02531.34270.70471.276141.42832.979735.7611
53.72050.82152.06283.55520.01333.4285-0.4376-0.3687-1.62220.61550.4342-0.53590.0599-0.03150.02980.70730.17340.05020.44720.06660.970545.52516.495915.9334
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 1125:1160)

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