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- PDB-5lpw: Crystal structure of the apo-BRI1 kinase domain (865-1160) -

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Basic information

Entry
Database: PDB / ID: 5lpw
TitleCrystal structure of the apo-BRI1 kinase domain (865-1160)
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 / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / non-specific serine/threonine protein kinase / endosome membrane / 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 ...: / 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
Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.431 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: 4OA6
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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BRASSINOSTEROID INSENSITIVE 1


Theoretical massNumber of molelcules
Total (without water)33,4421
Polymers33,4421
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.137, 116.137, 50.295
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 BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 20K/MME 550 morpheus mix, 0.12 M eth glycol mix, 0.1 M Hepes pH 7.5

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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: 2.43→19.36 Å / Num. obs: 14560 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.01 % / Biso Wilson estimate: 71.2 Å2 / CC1/2: 1 / Rsym value: 0.062 / Net I/σ(I): 28.56
Reflection shellResolution: 2.43→2.58 Å / Redundancy: 13.55 % / Mean I/σ(I) obs: 1.99 / CC1/2: 0.783 / % possible all: 91.5

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Processing

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

3uim


Resolution: 2.431→19.356 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.3
RfactorNum. reflection% reflection
Rfree0.2479 736 5.06 %
Rwork0.2035 --
obs0.2057 14555 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.431→19.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 0 10 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032215
X-RAY DIFFRACTIONf_angle_d0.6613003
X-RAY DIFFRACTIONf_dihedral_angle_d13.626806
X-RAY DIFFRACTIONf_chiral_restr0.023339
X-RAY DIFFRACTIONf_plane_restr0.003380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4308-2.61810.3621540.29842563X-RAY DIFFRACTION93
2.6181-2.88080.31351530.26292772X-RAY DIFFRACTION100
2.8808-3.29590.29971310.23872799X-RAY DIFFRACTION100
3.2959-4.14580.24011480.21182822X-RAY DIFFRACTION100
4.1458-19.35680.21691500.1712863X-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)
17.3422-4.1537-3.56488.07544.61575.37150.2806-0.44510.9936-0.48040.3464-0.1636-0.5610.4053-0.39880.54820.09210.05010.6499-0.03310.636730.69335.364618.1791
28.4509-0.0516-0.84256.99280.64764.0066-0.2149-0.1978-0.49930.32160.3487-0.2598-0.1550.1341-0.15020.58580.1105-0.02960.4024-0.06590.437642.814120.329115.5217
30.14250.87270.02465.3940.53361.6432-0.1232-2.8678-2.04461.2942-0.1702-1.84120.4381.34730.85081.40160.3-0.3071.51420.62851.455453.114410.219230.318
43.56510.40010.28073.52910.44935.183-0.2556-2.1094-2.05160.24480.06770.48341.51651.11610.25131.48210.0842-0.20571.72360.94211.600942.06632.566836.5397
53.45050.81893.46274.4341.05523.7848-0.3692-1.0583-2.23630.56880.2857-0.52130.1845-0.03650.08410.79520.17610.04030.63470.18711.24445.5916.264416.7338
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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