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- PDB-5feg: Crystal structure of the dimeric allergen profilin (Hev b 8) -

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Basic information

Entry
Database: PDB / ID: 5feg
TitleCrystal structure of the dimeric allergen profilin (Hev b 8)
ComponentsProfilin-2
KeywordsALLERGEN / Actin Binding Protein / Allergy / Cross-reactivity / Hev b 8
Function / homology
Function and homology information


: / actin binding / cytoskeleton / cytoplasm
Similarity search - Function
: / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsMares-Mejia, I. / Rodriguez-Romero, A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
DGAPA-UNAMIN207613 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)166472 Mexico
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into the IgE mediated responses induced by the allergens Hev b 8 and Zea m 12 in their dimeric forms.
Authors: Mares-Mejia, I. / Martinez-Caballero, S. / Garay-Canales, C. / Cano-Sanchez, P. / Torres-Larios, A. / Lara-Gonzalez, S. / Ortega, E. / Rodriguez-Romero, A.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Item: _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: Profilin-2
B: Profilin-2


Theoretical massNumber of molelcules
Total (without water)28,3242
Polymers28,3242
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.558, 58.558, 87.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Profilin-2 / / Pollen allergen Hev b 8.0102


Mass: 14162.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Clone RRIM600 / Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Tissue: Leaf / Gene: PRO2 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9STB6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M TRIS-HCl, pH 9.0; 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5416 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.8→43.86 Å / Num. obs: 8075 / % possible obs: 98.1 % / Redundancy: 2.6 % / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FDS

5fds


Resolution: 2.802→33.092 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 377 4.67 %RANDOM
Rwork0.2067 ---
obs0.2097 8075 98.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→33.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 0 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091957
X-RAY DIFFRACTIONf_angle_d1.2482664
X-RAY DIFFRACTIONf_dihedral_angle_d15.7391142
X-RAY DIFFRACTIONf_chiral_restr0.058290
X-RAY DIFFRACTIONf_plane_restr0.006354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8021-3.20680.34941390.28972552X-RAY DIFFRACTION94
3.2068-4.03720.24871160.22232604X-RAY DIFFRACTION95
4.0372-24.320.21621200.17252535X-RAY DIFFRACTION92

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