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- PDB-6a5a: Crystal structure of plant Receptor-like Kinase ANX1 -

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Basic information

Entry
Database: PDB / ID: 6a5a
TitleCrystal structure of plant Receptor-like Kinase ANX1
ComponentsReceptor-like protein kinase ANXUR1
KeywordsTRANSFERASE / a plant receptor
Function / homology
Function and homology information


pollen tube tip / transmembrane receptor protein tyrosine kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Receptor-like protein kinase ANXUR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å
AuthorsXiao, Y. / Chai, J.
CitationJournal: Nature / Year: 2019
Title: Mechanisms of RALF peptide perception by a heterotypic receptor complex.
Authors: Xiao, Y. / Stegmann, M. / Han, Z. / DeFalco, T.A. / Parys, K. / Xu, L. / Belkhadir, Y. / Zipfel, C. / Chai, J.
History
DepositionJun 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Receptor-like protein kinase ANXUR1
A: Receptor-like protein kinase ANXUR1


Theoretical massNumber of molelcules
Total (without water)85,7862
Polymers85,7862
Non-polymers00
Water00
1
B: Receptor-like protein kinase ANXUR1


Theoretical massNumber of molelcules
Total (without water)42,8931
Polymers42,8931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Receptor-like protein kinase ANXUR1


Theoretical massNumber of molelcules
Total (without water)42,8931
Polymers42,8931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.337, 77.546, 99.288
Angle α, β, γ (deg.)90.000, 100.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 26 - 408 / Label seq-ID: 1 - 383

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBA

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Components

#1: Protein Receptor-like protein kinase ANXUR1


Mass: 42893.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9SR05, non-specific serine/threonine protein kinase

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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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M BIS-Tris pH 6.5, 25%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 19284 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rsym value: 0.144 / Net I/σ(I): 17.2
Reflection shellResolution: 2.94→3.1 Å / Num. unique obs: 1750 / Rsym value: 0.481

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5C

6a5c


Resolution: 2.942→41.86 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.99 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2604 992 5.14 %
Rwork0.1963 --
obs0.1996 19284 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.39 Å2 / Biso mean: 29.8973 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 2.942→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 0 0 5920
Num. residues----752
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3534X-RAY DIFFRACTION9.445TORSIONAL
12B3534X-RAY DIFFRACTION9.445TORSIONAL
LS refinement shellResolution: 2.942→3.047 Å
RfactorNum. reflection% reflection
Rfree0.2936 --
Rwork0.2672 --
obs-1750 93 %

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