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- PDB-4eby: Crystal structure of the ectodomain of a receptor like kinase -

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Basic information

Entry
Database: PDB / ID: 4eby
TitleCrystal structure of the ectodomain of a receptor like kinase
ComponentsChitin elicitor receptor kinase 1
KeywordsTRANSFERASE / pathogen-associated molecular patterns / Pattern recognition receptors / Chitin Elicitor Receptor Kinase 1 / LysM / lysine motif / chitin oligomer
Function / homology
Function and homology information


cellular response to chitin / chitosan binding / transmembrane receptor protein kinase activity / response to chitin / detection of molecule of fungal origin / detection of peptidoglycan / cellular response to molecule of bacterial origin / cell surface pattern recognition receptor signaling pathway / chitin binding / defense response to fungus ...cellular response to chitin / chitosan binding / transmembrane receptor protein kinase activity / response to chitin / detection of molecule of fungal origin / detection of peptidoglycan / cellular response to molecule of bacterial origin / cell surface pattern recognition receptor signaling pathway / chitin binding / defense response to fungus / : / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / defense response to bacterium / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
LysM domain receptor kinase CERK1/LYK3-like / LysM domain / LysM domain profile. / LysM domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...LysM domain receptor kinase CERK1/LYK3-like / LysM domain / LysM domain profile. / LysM domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Similarity search - Domain/homology
Chitin elicitor receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChai, J. / Liu, T. / Han, Z. / She, J / Wang, J.
CitationJournal: Science / Year: 2012
Title: Chitin-induced dimerization activates a plant immune receptor.
Authors: Liu, T. / Liu, Z. / Song, C. / Hu, Y. / Han, Z. / She, J. / Fan, F. / Wang, J. / Jin, C. / Chang, J. / Zhou, J.M. / Chai, J.
History
DepositionMar 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin elicitor receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5376
Polymers23,4561
Non-polymers2,0815
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.829, 71.128, 72.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitin elicitor receptor kinase 1


Mass: 23456.076 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CERK1, At3g21630, AT3G21630 / Cell line (production host): sf-21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8R7E6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH6.5, 0.2M sodium acetate, 30% (v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.642→99 Å / Num. obs: 35917 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→23.213 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1788 4.98 %
Rwork0.1709 --
obs0.1718 35917 99.36 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.559 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1452 Å2-0 Å20 Å2
2---6.3401 Å2-0 Å2
3---6.195 Å2
Refinement stepCycle: LAST / Resolution: 1.65→23.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 137 348 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081732
X-RAY DIFFRACTIONf_angle_d1.2812353
X-RAY DIFFRACTIONf_dihedral_angle_d14.469664
X-RAY DIFFRACTIONf_chiral_restr0.083278
X-RAY DIFFRACTIONf_plane_restr0.007300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69460.26461370.23042590X-RAY DIFFRACTION100
1.6946-1.74450.22981230.20242593X-RAY DIFFRACTION100
1.7445-1.80070.20431400.17692585X-RAY DIFFRACTION100
1.8007-1.86510.20191360.16912622X-RAY DIFFRACTION100
1.8651-1.93970.18151300.16012615X-RAY DIFFRACTION100
1.9397-2.02790.19951350.15622618X-RAY DIFFRACTION100
2.0279-2.13480.18771560.16292607X-RAY DIFFRACTION100
2.1348-2.26840.17711270.15842645X-RAY DIFFRACTION100
2.2684-2.44340.19921180.16982639X-RAY DIFFRACTION100
2.4434-2.6890.2111450.16572655X-RAY DIFFRACTION100
2.689-3.07730.18511480.17612650X-RAY DIFFRACTION100
3.0773-3.87420.15021520.15622671X-RAY DIFFRACTION100
3.8742-23.21530.20491410.18522639X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 1.2693 Å / Origin y: -10.2439 Å / Origin z: -9.4443 Å
111213212223313233
T0.1222 Å20.0032 Å2-0.0034 Å2-0.1094 Å20.0031 Å2--0.1103 Å2
L1.4746 °20.0503 °2-0.189 °2-1.2579 °2-0.5596 °2--1.0743 °2
S0.0048 Å °0.0588 Å °0.0473 Å °-0.0018 Å °0.0111 Å °0.0433 Å °-0.0323 Å °0.0093 Å °-0.0006 Å °
Refinement TLS groupSelection details: ALL

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