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- PDB-4xuw: Structure of the hazelnut allergen, Cor a 8 -

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Basic information

Entry
Database: PDB / ID: 4xuw
TitleStructure of the hazelnut allergen, Cor a 8
ComponentsNon-specific lipid-transfer protein
KeywordsALLERGEN / plant protein
Function / homology
Function and homology information


seed development / lipid transport / lipid binding
Similarity search - Function
Plant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Non-specific lipid-transfer protein Cor a 8
Similarity search - Component
Biological speciesCorylus avellana (European hazelnut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsOffermann, L.R. / Perdue, M.L. / Bublin, M. / Pfeifer, S. / Dubiela, P. / Hoffmann-Sommergruber, K. / Chruszcz, M.
CitationJournal: J.Agric.Food Chem. / Year: 2015
Title: Structural and Functional Characterization of the Hazelnut Allergen Cor a 8.
Authors: Offermann, L.R. / Bublin, M. / Perdue, M.L. / Pfeifer, S. / Dubiela, P. / Borowski, T. / Chruszcz, M. / Hoffmann-Sommergruber, K.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific lipid-transfer protein
B: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0693
Polymers18,9742
Non-polymers951
Water5,549308
1
A: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5822
Polymers9,4871
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-specific lipid-transfer protein


Theoretical massNumber of molelcules
Total (without water)9,4871
Polymers9,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.678, 30.816, 56.184
Angle α, β, γ (deg.)90.00, 108.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 115 / Label seq-ID: 1 - 92

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Non-specific lipid-transfer protein / Cor a 8


Mass: 9487.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corylus avellana (European hazelnut) / References: UniProt: Q9ATH2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 1.71 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic, pH 6.9
PH range: 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 47711 / Num. obs: 47711 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 37.4
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 8.51 / % possible all: 49.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ALG

2alg


Resolution: 1.1→23.83 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.273 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17696 2433 5.1 %RANDOM
Rwork0.1424 45211 --
obs0.14419 45211 90.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.235 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å2-0.38 Å2
2---0.02 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.1→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 5 308 1621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021403
X-RAY DIFFRACTIONr_bond_other_d0.0030.021409
X-RAY DIFFRACTIONr_angle_refined_deg2.3492.011928
X-RAY DIFFRACTIONr_angle_other_deg2.3353.013262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50425.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.54157
X-RAY DIFFRACTIONr_chiral_restr0.1270.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211611
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02268
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.45631395
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.67751358
Refine LS restraints NCS

Ens-ID: 1 / Number: 5070 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 100 -
Rwork0.195 1845 -
obs--50.65 %

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