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- PDB-5xkn: Crystal structure of plant receptor ERL2 in complexe with EPFL4 -

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Basic information

Entry
Database: PDB / ID: 5xkn
TitleCrystal structure of plant receptor ERL2 in complexe with EPFL4
Components
  • EPIDERMAL PATTERNING FACTOR-like protein 4
  • LRR receptor-like serine/threonine-protein kinase ERL2
KeywordsTRANSFERASE/SIGNALING PROTEIN / receptor like kinase / peptide hormone EPFL4 / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


guard cell differentiation / stomatal complex morphogenesis / plant ovule development / embryo sac development / stomatal complex development / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding ...guard cell differentiation / stomatal complex morphogenesis / plant ovule development / embryo sac development / stomatal complex development / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / identical protein binding / membrane
Similarity search - Function
EPIDERMAL PATTERNING FACTOR-like protein / Epidermal patterning factor proteins / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeats (2 copies) / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype ...EPIDERMAL PATTERNING FACTOR-like protein / Epidermal patterning factor proteins / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeats (2 copies) / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
Similarity search - Domain/homology
EPIDERMAL PATTERNING FACTOR-like protein 4 / LRR receptor-like serine/threonine-protein kinase ERL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.651 Å
AuthorsChai, J. / Lin, G.
CitationJournal: Genes Dev. / Year: 2017
Title: A receptor-like protein acts as a specificity switch for the regulation of stomatal development.
Authors: Lin, G. / Zhang, L. / Han, Z. / Yang, X. / Liu, W. / Li, E. / Chang, J. / Qi, Y. / Shpak, E.D. / Chai, J.
History
DepositionMay 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: EPIDERMAL PATTERNING FACTOR-like protein 4
A: LRR receptor-like serine/threonine-protein kinase ERL2
B: LRR receptor-like serine/threonine-protein kinase ERL2
F: EPIDERMAL PATTERNING FACTOR-like protein 4


Theoretical massNumber of molelcules
Total (without water)131,7384
Polymers131,7384
Non-polymers00
Water00
1
E: EPIDERMAL PATTERNING FACTOR-like protein 4
B: LRR receptor-like serine/threonine-protein kinase ERL2


Theoretical massNumber of molelcules
Total (without water)65,8692
Polymers65,8692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-4 kcal/mol
Surface area24360 Å2
MethodPISA
2
A: LRR receptor-like serine/threonine-protein kinase ERL2
F: EPIDERMAL PATTERNING FACTOR-like protein 4


Theoretical massNumber of molelcules
Total (without water)65,8692
Polymers65,8692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-4 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.995, 112.330, 175.368
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 EPIDERMAL PATTERNING FACTOR-like protein 4 / CHALLAH-LIKE21 / EPF-like protein 4


Mass: 5656.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EPFL4, CLL2, At4g14723, FCAALL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2V3I3
#2: Protein LRR receptor-like serine/threonine-protein kinase ERL2 / Protein ERECTA-like kinase 2


Mass: 60212.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ERL2, At5g07180, T28J14.120 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6XAT2, non-specific serine/threonine protein kinase
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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.0, 10% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 21816 / % possible obs: 89.6 % / Redundancy: 3.5 % / Net I/σ(I): 13.8
Reflection shellResolution: 3.6507→3.8168 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.651→47.295 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3125 1119 5.14 %
Rwork0.2823 --
obs0.2838 21781 88.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.651→47.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8824 0 0 0 8824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049024
X-RAY DIFFRACTIONf_angle_d0.91812282
X-RAY DIFFRACTIONf_dihedral_angle_d14.6035408
X-RAY DIFFRACTIONf_chiral_restr0.051421
X-RAY DIFFRACTIONf_plane_restr0.0061605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6507-3.81680.43921230.39582352X-RAY DIFFRACTION82
3.8168-4.01790.3271330.31072558X-RAY DIFFRACTION89
4.0179-4.26950.31631460.27692525X-RAY DIFFRACTION89
4.2695-4.59890.32771330.28262544X-RAY DIFFRACTION88
4.5989-5.06120.33081330.25422563X-RAY DIFFRACTION89
5.0612-5.79250.33051500.28582604X-RAY DIFFRACTION89
5.7925-7.29360.34091560.29842701X-RAY DIFFRACTION92
7.2936-47.29850.24811450.25312815X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 42.9125 Å / Origin y: 10.786 Å / Origin z: 51.5861 Å
111213212223313233
T0.9985 Å2-0.055 Å2-0.0092 Å2-0.9156 Å2-0.0495 Å2--0.9358 Å2
L0.1381 °2-0.0233 °2-0.0517 °2-0.5096 °2-0.1915 °2--0.4657 °2
S-0.0297 Å °0.005 Å °0.0219 Å °-0.0981 Å °0.0092 Å °0.1147 Å °0.1594 Å °0.0101 Å °0.011 Å °
Refinement TLS groupSelection details: all

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