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- PDB-5yah: Crystal 2 for AtLURE1.2-AtPRK6LRR -

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Basic information

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


pollen tube guidance / pollen tube tip / protein phosphorylation / 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 / Protein kinase 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 / Protein kinase domain / 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 / Resolution: 2.104 Å
AuthorsChai, J. / Zhang, X.
Funding support China, 2items
OrganizationGrant numberCountry
Department of S and T for Social Development2015CB910200 China
National Science Foundation of China31421001 China
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 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Pollen receptor-like kinase 6
C: Protein LURE 1.2


Theoretical massNumber of molelcules
Total (without water)35,1442
Polymers35,1442
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-3 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.706, 43.347, 77.821
Angle α, β, γ (deg.)90.00, 124.70, 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.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MgCl2, Bis-Tris pH 5.5, 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: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.104→31.992 Å / Num. obs: 15868 / % possible obs: 99.7 % / Redundancy: 4.6 % / Net I/σ(I): 30.5
Reflection shellResolution: 2.104→2.24 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.104→31.992 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 0 / Phase error: 33.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 790 4.98 %
Rwork0.2239 --
obs0.226 15858 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.104→31.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 44 2027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082030
X-RAY DIFFRACTIONf_angle_d1.2252726
X-RAY DIFFRACTIONf_dihedral_angle_d14.649770
X-RAY DIFFRACTIONf_chiral_restr0.089306
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1044-2.23620.37361110.31712482X-RAY DIFFRACTION98
2.2362-2.40890.38041350.29882506X-RAY DIFFRACTION100
2.4089-2.65120.351390.26662467X-RAY DIFFRACTION100
2.6512-3.03450.31761360.26682512X-RAY DIFFRACTION100
3.0345-3.82220.25911220.22352548X-RAY DIFFRACTION100
3.8222-31.99530.21511470.18132553X-RAY DIFFRACTION99

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