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- PDB-5fef: Crystal structure of the allergen profilin (Zea m 12) -

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Basic information

Entry
Database: PDB / ID: 5fef
TitleCrystal structure of the allergen profilin (Zea m 12)
ComponentsProfilin-5
KeywordsALLERGEN / Actin-binding protein / Allergy / Cross-reactivity / Zea m 12
Function / homology
Function and homology information


phospholipase C-inhibiting G protein-coupled receptor signaling pathway / sequestering of actin monomers / proline-rich region binding / nuclear migration / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / regulation of actin cytoskeleton organization / cell cortex / cytoskeleton
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 speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMares-Mejia, I. / Rodriguez-Romero, A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
DGAPAIN207613 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 16, 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-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6446
Polymers14,1831
Non-polymers4605
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.531, 58.531, 135.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Profilin-5 / Pollen allergen Zea m 12 / ZmPRO5


Mass: 14183.159 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Tissue: leaf / Gene: PRO5 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9FR39
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M TRIS-HCL, pH 9.0, 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5416 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.2→44.25 Å / Num. obs: 12462 / % possible obs: 99.2 % / Observed criterion σ(F): 1.3 / Redundancy: 4.5 % / Biso Wilson estimate: 37.03 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FDS

5fds


Resolution: 2.2→44.25 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 630 5.06 %RANDOM
Rwork0.2184 ---
obs0.2197 12454 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 30 32 1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081061
X-RAY DIFFRACTIONf_angle_d1.2071434
X-RAY DIFFRACTIONf_dihedral_angle_d14.408396
X-RAY DIFFRACTIONf_chiral_restr0.044154
X-RAY DIFFRACTIONf_plane_restr0.005186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.42150.33821540.29482841X-RAY DIFFRACTION98
2.4215-2.77190.35461310.28262916X-RAY DIFFRACTION99
2.7719-3.4920.2911670.24562936X-RAY DIFFRACTION99
3.492-44.250.19311780.17963131X-RAY DIFFRACTION100

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