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- PDB-5wls: Crystal Structure of a Pollen Receptor Kinase 3 -

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Basic information

Entry
Database: PDB / ID: 5wls
TitleCrystal Structure of a Pollen Receptor Kinase 3
ComponentsPollen receptor-like kinase 3
KeywordsPLANT PROTEIN / Pollen Receptor Kinase / Leucine Rich Repeat / Extracellular Domain / Receptor Like Kinase
Function / homology
Function and homology information


regulation of pollen tube growth / protein serine/threonine kinase activity => GO:0004674 / plasmodesma / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
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 / 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 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsXu, G. / Chakraborty, S. / Pan, H.
CitationJournal: Sci Rep / Year: 2018
Title: The Extracellular Domain of Pollen Receptor Kinase 3 is structurally similar to the SERK family of co-receptors.
Authors: Chakraborty, S. / Pan, H. / Tang, Q. / Woolard, C. / Xu, G.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pollen receptor-like kinase 3
B: Pollen receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5386
Polymers46,2472
Non-polymers1,2914
Water1,67593
1
A: Pollen receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7693
Polymers23,1231
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pollen receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7693
Polymers23,1231
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.061, 72.061, 125.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

21B-430-

HOH

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Components

#1: Protein Pollen receptor-like kinase 3 / AtPRK3


Mass: 23123.357 Da / Num. of mol.: 2 / Fragment: UNP residues 26-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRK3, At3g42880, F18P9.40
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9M1L7, non-specific serine/threonine protein kinase
#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.: 2
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, pH 8.0, 18% PEG3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0422 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0422 Å / Relative weight: 1
ReflectionResolution: 2.496→36.22 Å / Num. obs: 22282 / % possible obs: 99.83 % / Redundancy: 7.5 % / Net I/σ(I): 24.52

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lsx

4lsx


Resolution: 2.496→36.22 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 32.34
RfactorNum. reflection% reflection
Rfree0.2766 1089 4.89 %
Rwork0.2464 --
obs0.248 22269 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.496→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 84 93 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063342
X-RAY DIFFRACTIONf_angle_d1.3164537
X-RAY DIFFRACTIONf_dihedral_angle_d5.7982025
X-RAY DIFFRACTIONf_chiral_restr0.068530
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4959-2.60950.35391390.26522611X-RAY DIFFRACTION100
2.6095-2.7470.38221070.28032681X-RAY DIFFRACTION100
2.747-2.91910.3729820.28312691X-RAY DIFFRACTION100
2.9191-3.14440.34481460.29022638X-RAY DIFFRACTION100
3.1444-3.46070.3331370.28072632X-RAY DIFFRACTION100
3.4607-3.9610.29171370.23532642X-RAY DIFFRACTION100
3.961-4.98890.20341640.19432644X-RAY DIFFRACTION100
4.9889-39.5830.25451770.24812641X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -54.0593 Å / Origin y: 16.9186 Å / Origin z: 11.3137 Å
111213212223313233
T0.3188 Å2-0.0101 Å20.0273 Å2-0.4079 Å2-0.0639 Å2--0.2997 Å2
L0.8611 °2-0.6424 °20.4459 °2-2.1985 °2-0.8434 °2--0.5786 °2
S-0.1165 Å °-0.0688 Å °0.0405 Å °0.0332 Å °0.1642 Å °-0.0449 Å °-0.0502 Å °-0.0595 Å °0.0035 Å °
Refinement TLS groupSelection details: all

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