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- PDB-5y9w: Crystal 1 for AtLURE1.2-AtPRK6LRR -

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Basic information

Entry
Database: PDB / ID: 5y9w
TitleCrystal 1 for AtLURE1.2-AtPRK6LRR
Components
  • Pollen receptor-like kinase 6
  • Protein LURE 1.2
KeywordsTRANSFERASE / Cysteine-rich peptide / Leucine-rich repeat receptor kinase / Receptor-ligand complex / Pollen tube guidance / PLANT PROTEIN
Function / homology
Function and homology information


pollen tube tip / pollen tube guidance / protein serine/threonine kinase activity / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
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, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...: / : / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Pollen receptor-like kinase 6 / Protein LURE 1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.847 Å
AuthorsChai, J. / Zhang, X.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for receptor recognition of pollen tube attraction peptides.
Authors: Zhang, X. / Liu, W. / Nagae, T.T. / Takeuchi, H. / Zhang, H. / Han, Z. / Higashiyama, T. / Chai, J.
History
DepositionAug 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 6, 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
B: Pollen receptor-like kinase 6
C: Protein LURE 1.2
A: Pollen receptor-like kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,76710
Polymers62,0943
Non-polymers6727
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-107 kcal/mol
Surface area22670 Å2
Unit cell
Length a, b, c (Å)96.687, 48.511, 146.310
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pollen receptor-like kinase 6 / AtPRK6


Mass: 26950.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRK6, At5g20690, T1M15.90 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q3E991
#2: Protein Protein LURE 1.2 / AtLURE1.2 / Cysteine-Rich Peptide 810_1.2 / CRP810_1.2 / Defensin-like protein 213


Mass: 8193.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LURE1.2, CRP810_1.2, At5g43510, MWF20.23 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4VP08
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.847→35.383 Å / Num. obs: 56086 / % possible obs: 98.2 % / Redundancy: 3.7 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
Blu-Icedata collection
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MN8

4mn8


Resolution: 1.847→35.383 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 0 / Phase error: 22.86
RfactorNum. reflection% reflection
Rfree0.2408 2845 5.07 %
Rwork0.2042 --
obs0.206 56074 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.847→35.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 35 382 4062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093744
X-RAY DIFFRACTIONf_angle_d0.9465055
X-RAY DIFFRACTIONf_dihedral_angle_d16.8422287
X-RAY DIFFRACTIONf_chiral_restr0.058564
X-RAY DIFFRACTIONf_plane_restr0.008646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8472-1.87910.27831440.2512534X-RAY DIFFRACTION94
1.8791-1.91330.28781380.24572598X-RAY DIFFRACTION98
1.9133-1.95010.26021490.23462653X-RAY DIFFRACTION97
1.9501-1.98990.2361310.20642651X-RAY DIFFRACTION99
1.9899-2.03310.23281270.20762672X-RAY DIFFRACTION98
2.0331-2.08040.23111400.20112646X-RAY DIFFRACTION97
2.0804-2.13240.23871710.20592567X-RAY DIFFRACTION98
2.1324-2.19010.21821320.20322593X-RAY DIFFRACTION96
2.1901-2.25450.24871450.19912661X-RAY DIFFRACTION98
2.2545-2.32730.2311360.1972666X-RAY DIFFRACTION99
2.3273-2.41040.23271190.20742718X-RAY DIFFRACTION99
2.4104-2.50690.24551450.21142655X-RAY DIFFRACTION99
2.5069-2.6210.2791510.21372665X-RAY DIFFRACTION99
2.621-2.75910.24561520.2222651X-RAY DIFFRACTION97
2.7591-2.93190.2531500.21382644X-RAY DIFFRACTION98
2.9319-3.15820.24851430.22132713X-RAY DIFFRACTION99
3.1582-3.47570.24321400.20282740X-RAY DIFFRACTION100
3.4757-3.97810.23211380.18512709X-RAY DIFFRACTION99
3.9781-5.00970.20641580.17242696X-RAY DIFFRACTION98
5.0097-35.38920.26221360.22042797X-RAY DIFFRACTION98

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