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- PDB-6gre: Crystal structure of the tandem DUF26 ectodomain from the Arabido... -

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Basic information

Entry
Database: PDB / ID: 6gre
TitleCrystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.
ComponentsCysteine-rich repeat secretory protein 2
KeywordsSIGNALING PROTEIN / lectin / membrane protein / DUF26 domain / disulfide bond / plasmodesmata / immune signaling
Function / homology
Function and homology information


plasmodesma / response to other organism / defense response to bacterium / plasma membrane
Similarity search - Function
Gnk2-homologous domain / Gnk2-homologous domain superfamily / : / Salt stress response/antifungal / Gnk2-homologous domain profile.
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / Plasmodesmata-located protein 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.29 Å
AuthorsBrandt, B. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_176237 Switzerland
CitationJournal: Commun Biol / Year: 2019
Title: Mechanistic insights into the evolution of DUF26-containing proteins in land plants.
Authors: Vaattovaara, A. / Brandt, B. / Rajaraman, S. / Safronov, O. / Veidenberg, A. / Luklova, M. / Kangasjarvi, J. / Loytynoja, A. / Hothorn, M. / Salojarvi, J. / Wrzaczek, M.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_conn_angle / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine-rich repeat secretory protein 2
B: Cysteine-rich repeat secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,82119
Polymers48,4282
Non-polymers2,39317
Water5,585310
1
A: Cysteine-rich repeat secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2279
Polymers24,2141
Non-polymers1,0138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine-rich repeat secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,59410
Polymers24,2141
Non-polymers1,3809
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.760, 47.970, 62.190
Angle α, β, γ (deg.)97.70, 102.72, 99.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine-rich repeat secretory protein 2 / Cysteine-rich repeat protein HWI1 / Plasmodesmata-located protein 5 / PDLP5 / Protein HOPW1-1-INDUCED 1


Mass: 24213.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRRSP2, HWI1, At1g70690, F5A18.13 / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao / References: UniProt: Q8GUJ2

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Sugars , 2 types, 4 molecules

#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.: 3
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 323 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 17.5 % polyethylene glycol 4,000, 250 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.29→37.77 Å / Num. obs: 108820 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / CC1/2: 0.999 / Rrim(I) all: 0.049 / Rsym value: 0.041 / Net I/σ(I): 12.56
Reflection shellResolution: 1.29→1.32 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 7623 / CC1/2: 0.557 / Rrim(I) all: 1.29 / Rsym value: 1.1 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.29→37.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.206 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20988 5441 5 %RANDOM
Rwork0.18645 ---
obs0.18762 103379 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.06 Å20.47 Å2
2---0.51 Å2-0.94 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.29→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 153 310 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143446
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182956
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.7074720
X-RAY DIFFRACTIONr_angle_other_deg1.0831.7077008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57523.75152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57215533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.811514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8892.141730
X-RAY DIFFRACTIONr_mcbond_other1.8872.1381729
X-RAY DIFFRACTIONr_mcangle_it2.9833.1992180
X-RAY DIFFRACTIONr_mcangle_other2.9833.22181
X-RAY DIFFRACTIONr_scbond_it2.5922.6071716
X-RAY DIFFRACTIONr_scbond_other2.5652.5941709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9933.7842501
X-RAY DIFFRACTIONr_long_range_B_refined5.48827.9294002
X-RAY DIFFRACTIONr_long_range_B_other5.45427.6243938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.289→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 381 -
Rwork0.347 7248 -
obs--89.52 %

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