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- PDB-8h3j: Crystal Structure of Pathogenesis-related Protein HcPR10 from Hal... -

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Basic information

Entry
Database: PDB / ID: 8h3j
TitleCrystal Structure of Pathogenesis-related Protein HcPR10 from Halostachys caspica in complex with trans-Zeatin-riboside
ComponentsPR10
KeywordsALLERGEN / Pathogenesis-related Protein / Halostachys caspica / reservoir for cytokinin
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
N-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]adenosine / PR10
Similarity search - Component
Biological speciesHalostachys caspica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, Z. / Ren, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32125008 China
CitationJournal: Front Plant Sci / Year: 2023
Title: Halostachys caspica pathogenesis-related protein 10 acts as a cytokinin reservoir to regulate plant growth and development.
Authors: Feng, Y. / Ren, Y. / Zhang, H. / Heng, Y. / Wang, Z. / Wang, Y.
History
DepositionOct 8, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Jul 17, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PR10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5312
Polymers18,1801
Non-polymers3511
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.460, 59.460, 91.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

#1: Protein PR10


Mass: 18179.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halostachys caspica (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A171NYA8
#2: Chemical ChemComp-Q3V / N-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]adenosine


Mass: 351.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES sodium 7.5;1.4M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 19482 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 27.33 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 35.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 922

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BV1

1bv1


Resolution: 1.75→34.23 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.4222 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2309 990 5.09 %
Rwork0.2089 18451 -
obs0.2101 19441 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 25 101 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341329
X-RAY DIFFRACTIONf_angle_d0.6731806
X-RAY DIFFRACTIONf_chiral_restr0.0515201
X-RAY DIFFRACTIONf_plane_restr0.004233
X-RAY DIFFRACTIONf_dihedral_angle_d22.6234478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.840.34861000.27552609X-RAY DIFFRACTION100
1.84-1.960.27971450.23942576X-RAY DIFFRACTION100
1.96-2.110.29651300.21832627X-RAY DIFFRACTION100
2.11-2.320.24171400.21892607X-RAY DIFFRACTION100
2.32-2.660.24861620.22012601X-RAY DIFFRACTION100
2.66-3.350.21681490.21992667X-RAY DIFFRACTION100
3.35-34.230.2071640.18692764X-RAY DIFFRACTION99.86

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