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

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Basic information

Entry
Database: PDB / ID: 5lpb
TitleCrystal structure of the BRI1 kinase domain (865-1160) 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 / 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'-DIPHOSPHATE / Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 12, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionAug 31, 2016ID: 4OAC
Revision 1.0Aug 31, 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)33,8692
Polymers33,4421
Non-polymers4271
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint3 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.141, 116.141, 49.743
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 / Fragment: UNP residues 865-1160 / 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.: 22 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 20K/MME 550 morpheus mix 0.12 M eth glycol mix 0.1 M Hepes pH 7 1mM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.98→44.58 Å / Num. obs: 26940 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 66.7 Å2 / CC1/2: 1 / Rsym value: 0.036 / Net I/σ(I): 24.28
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.71 / CC1/2: 0.836 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UIM

3uim


Resolution: 1.98→44.58 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2032 1385 5.15 %
Rwork0.1828 --
obs0.1838 26902 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 20 22 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042237
X-RAY DIFFRACTIONf_angle_d0.7923039
X-RAY DIFFRACTIONf_dihedral_angle_d12.6801
X-RAY DIFFRACTIONf_chiral_restr0.029343
X-RAY DIFFRACTIONf_plane_restr0.003383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9801-2.05080.32791330.33272532X-RAY DIFFRACTION100
2.0508-2.13290.34211470.2692527X-RAY DIFFRACTION100
2.1329-2.230.30411380.25312528X-RAY DIFFRACTION100
2.23-2.34760.26021490.22712514X-RAY DIFFRACTION100
2.3476-2.49460.24261360.19662544X-RAY DIFFRACTION100
2.4946-2.68720.24251530.20072532X-RAY DIFFRACTION100
2.6872-2.95760.21891390.19662551X-RAY DIFFRACTION100
2.9576-3.38550.22171240.19952566X-RAY DIFFRACTION100
3.3855-4.26480.18341290.17752579X-RAY DIFFRACTION100
4.2648-44.59940.17911370.16192644X-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)
15.8028-4.1285-2.34658.50193.46615.15990.2304-0.21330.6964-0.39850.0434-0.2852-0.33620.2156-0.16260.45130.05610.04910.54570.01340.611131.078535.727717.3913
28.0835-1.3689-1.87347.20520.98734.6386-0.1198-0.2769-0.13330.30390.2251-0.3586-0.10640.2341-0.12860.54990.0685-0.01240.3656-0.04840.472342.570220.509114.209
33.60150.7189-0.89813.1557-4.7467.1456-0.6044-1.3472-0.05931.85390.014-0.79090.04292.13760.86951.01560.2524-0.23421.29810.31940.932654.761212.732528.2975
43.51952.60991.14533.34630.06233.3827-0.3655-1.0614-1.87940.92130.1308-0.36220.63310.11930.17460.90760.27540.00520.61960.23490.996944.90116.553520.1585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 867:969)
2X-RAY DIFFRACTION2(chain A and resseq 970:1083)
3X-RAY DIFFRACTION3(chain A and resseq 1084:1112)
4X-RAY DIFFRACTION4(chain A and resseq 1113:1160)

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