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- PDB-7p20: High resolution structure of the Juniperus ashei allergen - Jun a 3 -

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Basic information

Entry
Database: PDB / ID: 7p20
TitleHigh resolution structure of the Juniperus ashei allergen - Jun a 3
ComponentsPathogenesis-related 5 protein Jun a 3.0101
KeywordsALLERGEN / Thaumatin-like protein / Juniperus Ashei
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
Pathogenesis-related 5 protein Jun a 3.0101
Similarity search - Component
Biological speciesJuniperus ashei (Ozark white cedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEder, M. / Hofer, G. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundF 4604-B19 Austria
CitationJournal: To Be Published
Title: Crystal structure of the allergen Jun a 3 the Thaumatin-like protein of Juniperus ashei
Authors: Eder, M. / Hofer, G. / Keller, W.
History
DepositionJul 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pathogenesis-related 5 protein Jun a 3.0101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0923
Polymers22,0211
Non-polymers712
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.424, 49.317, 71.447
Angle α, β, γ (deg.)90.000, 104.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21A-491-

HOH

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Components

#1: Protein Pathogenesis-related 5 protein Jun a 3.0101 / PR-5 protein Jun a 3.0101 / Pollen allergen Jun a 3 / Jun a 3


Mass: 22021.402 Da / Num. of mol.: 1 / Mutation: N133Q, N188Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Juniperus ashei (Ozark white cedar) / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / Tissue (production host): Kidney (Embryonic) / References: UniProt: P81295
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.31 % / Description: big leaflets
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: Index condition F5 (0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, and 17% w/v Polyethylene glycol 10,000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2543 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2543 Å / Relative weight: 1
ReflectionResolution: 1.4→35.34 Å / Num. obs: 34665 / % possible obs: 99.68 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09554 / Rpim(I) all: 0.04089 / Rrim(I) all: 0.1041 / Net I/σ(I): 18.44
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.1447 / Mean I/σ(I) obs: 11.95 / Num. unique obs: 3393 / CC1/2: 0.984 / Rpim(I) all: 0.06866 / Rrim(I) all: 0.1608 / % possible all: 97.67

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ahn

2ahn


Resolution: 1.4→35.34 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1638 1085 3.13 %
Rwork0.1351 33582 -
obs0.1361 34665 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.15 Å2 / Biso mean: 17.2939 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: final / Resolution: 1.4→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 2 290 1796
Biso mean--41.01 35.64 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.460.16541300.11754020415097
1.46-1.540.15351360.111742214357100
1.54-1.640.16691360.11642214357100
1.64-1.760.18811350.121241704305100
1.76-1.940.16741360.128642084344100
1.94-2.220.16341360.129542174353100
2.22-2.80.1761370.150342334370100
2.8-35.340.15281390.144342924431100

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