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- PDB-4l68: Structure of the psedudokinase domain of BIR2, an immune regulato... -

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Basic information

Entry
Database: PDB / ID: 4l68
TitleStructure of the psedudokinase domain of BIR2, an immune regulator of the RLK/Pelle family
ComponentsLeucine-rich repeat protein kinase-like protein
KeywordsSIGNALING PROTEIN / pseudokinase / negative immune regulator
Function / homology
Function and homology information


regulation of defense response to fungus / negative regulation of defense response to bacterium / chloroplast / defense response / nucleotide binding / plasma membrane / cytosol
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,3-PROPANDIOL / Inactive LRR receptor-like serine/threonine-protein kinase BIR2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBlaum, B.S. / Stehle, T.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structure of the pseudokinase domain of BIR2, a regulator of BAK1-mediated immune signaling in Arabidopsis.
Authors: Blaum, B.S. / Mazzotta, S. / Noldeke, E.R. / Halter, T. / Madlung, J. / Kemmerling, B. / Stehle, T.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat protein kinase-like protein
B: Leucine-rich repeat protein kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8163
Polymers75,7402
Non-polymers761
Water7,656425
1
A: Leucine-rich repeat protein kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9462
Polymers37,8701
Non-polymers761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich repeat protein kinase-like protein


Theoretical massNumber of molelcules
Total (without water)37,8701
Polymers37,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.141, 108.141, 392.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-968-

HOH

31B-898-

HOH

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Components

#1: Protein Leucine-rich repeat protein kinase-like protein / / BIR2 / Leucine-rich repeat receptor-like protein kinase / Putative receptor kinase / Receptor-like ...BIR2 / Leucine-rich repeat receptor-like protein kinase / Putative receptor kinase / Receptor-like protein kinase-like protein


Mass: 37869.934 Da / Num. of mol.: 2 / Fragment: cytosolic domain (UNP residues 271-605)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT3G28450, At3g28450/MFJ20_13, LRR-RLK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LSI9
#2: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M n-ethylene glycols, 0.1 M bicine/Trizma base, 10% PEG20000, 20% PEG550 MME, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2012
RadiationMonochromator: Bartels DCCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2→48.122 Å / Num. all: 60598 / Num. obs: 60269 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 33.8 Å2
Reflection shellResolution: 2→2.19 Å / % possible all: 23.52

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Processing

Software
NameVersionClassification
TVXdata collection
CCP4model building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.122 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 3013 5 %RANDOM
Rwork0.1751 ---
all0.191 60598 --
obs0.177 60266 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 5 425 5387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085149
X-RAY DIFFRACTIONf_angle_d0.9826970
X-RAY DIFFRACTIONf_chiral_restr0.07775
X-RAY DIFFRACTIONf_plane_restr0.004901
X-RAY DIFFRACTIONf_dihedral_angle_d13.8521902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.03130.29321350.280825542689
2.0313-2.06460.29841350.261825812716
2.0646-2.10020.26971350.243425572692
2.1002-2.13840.27651350.232925752710
2.1384-2.17950.25591360.216325762712
2.1795-2.2240.23321350.195125732708
2.224-2.27230.22981360.196625802716
2.2723-2.32520.26991360.189425692705
2.3252-2.38330.24181350.184925822717
2.3833-2.44780.23621370.174925892726
2.4478-2.51980.21611360.174825922728
2.5198-2.60110.21871360.179325822718
2.6011-2.69410.24331360.175225892725
2.6941-2.80190.24221360.176625812717
2.8019-2.92940.21531380.189526222760
2.9294-3.08390.22311370.182825972734
3.0839-3.2770.20831370.174626142751
3.277-3.530.20921370.170425952732
3.53-3.88510.22191380.155326302768
3.8851-4.44690.16371390.136826362775
4.4469-5.60130.16591410.15126802821
5.6013-48.1360.20281470.180527992946
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)
12.3532-0.3856-0.23882.26660.31491.5963-0.15150.14250.1189-0.1760.04070.0322-0.15140.17410.10.2567-0.0541-0.07420.19490.07390.09938.213120.80518.5435
23.0806-3.46681.02834.0491-1.37720.6786-0.12880.93880.969-0.44470.0122-0.4245-0.24010.16640.03890.8174-0.2193-0.1530.64540.29280.767910.029541.760912.2096
31.7814-0.95910.75531.3375-0.24450.9916-0.595-0.05331.3042-0.44610.03460.9511-0.736-0.23610.06470.73340.0351-0.4020.3120.10320.8126-9.748241.75118.4427
45.1846-0.66670.74797.7207-2.43127.7825-0.1435-0.82840.04640.2490.1860.7221-0.0263-0.75480.2330.42860.076-0.07750.4932-0.030.3341-2.596233.679436.5774
52.43640.1467-0.21062.4559-0.55143.51130.023-0.03210.02920.13250.06390.3786-0.196-0.6201-0.01150.1626-0.0343-0.04230.24770.03170.21769.690523.146854.5647
64.389-0.1753-0.64875.59110.35645.8378-0.0552-1.0625-0.42140.3331-0.0473-0.32140.43280.57770.11770.32310.0121-0.01190.37660.15940.345229.75410.37258.6026
73.4041-0.24010.08861.68470.33551.7226-0.10110.0177-0.3034-0.17250.06880.04230.0907-0.05680.02630.1202-0.05-0.00420.154-0.01650.150429.131218.659746.1523
83.6420.6895-0.03362.0743-1.77571.5925-0.18921.20130.0212-0.82070.09530.1027-1.2084-0.3550.02960.7265-0.1608-0.03510.5468-0.00960.425125.839735.467334.1793
93.6096-0.68220.25092.220.11951.5093-0.0268-0.1382-0.29320.052-0.0126-0.07360.11060.20890.02520.1305-0.03090.00980.15340.02180.120744.97519.262251.9123
105.1542-0.4151.46571.0720.00112.97950.00760.3462-0.7157-0.3230.07080.10660.06420.22880.01340.2678-0.03190.00290.3424-0.05840.22736.527919.058435.8084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 272 through 453 )
2X-RAY DIFFRACTION2chain 'A' and (resid 454 through 486 )
3X-RAY DIFFRACTION3chain 'A' and (resid 487 through 580 )
4X-RAY DIFFRACTION4chain 'A' and (resid 581 through 600 )
5X-RAY DIFFRACTION5chain 'B' and (resid 266 through 380 )
6X-RAY DIFFRACTION6chain 'B' and (resid 381 through 399 )
7X-RAY DIFFRACTION7chain 'B' and (resid 400 through 450 )
8X-RAY DIFFRACTION8chain 'B' and (resid 451 through 480 )
9X-RAY DIFFRACTION9chain 'B' and (resid 481 through 559 )
10X-RAY DIFFRACTION10chain 'B' and (resid 560 through 600 )

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