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- PDB-4x9u: Crystal structure of the kiwifruit allergen Act d 5 -

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Basic information

Entry
Database: PDB / ID: 4x9u
TitleCrystal structure of the kiwifruit allergen Act d 5
ComponentsKiwellin
KeywordsPLANT PROTEIN / Allergen
Function / homologyKiwellin-like / RlpA-like domain superfamily / extracellular region / Kiwellin
Function and homology information
Biological speciesActinidia deliciosa (kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOffermann, L.R. / Perdue, M.L. / Giangrieco, I. / Tamburrini, M. / Ciardiello, M.A. / Chruszcz, M.
CitationJournal: J.Agric.Food Chem. / Year: 2015
Title: Elusive Structural, Functional, and Immunological Features of Act d 5, the Green Kiwifruit Kiwellin.
Authors: Offermann, L.R. / Giangrieco, I. / Perdue, M.L. / Zuzzi, S. / Santoro, M. / Tamburrini, M. / Cosgrove, D.J. / Mari, A. / Ciardiello, M.A. / Chruszcz, M.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kiwellin
B: Kiwellin


Theoretical massNumber of molelcules
Total (without water)39,8342
Polymers39,8342
Non-polymers00
Water4,414245
1
A: Kiwellin


Theoretical massNumber of molelcules
Total (without water)19,9171
Polymers19,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kiwellin


Theoretical massNumber of molelcules
Total (without water)19,9171
Polymers19,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.392, 60.417, 55.601
Angle α, β, γ (deg.)90.00, 95.85, 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: GLY / Beg label comp-ID: GLY / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 47 - 188 / Label seq-ID: 47 - 188

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

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Components

#1: Protein Kiwellin


Mass: 19916.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Actinidia deliciosa (kiwifruit) / References: UniProt: P84527
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.19 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 25% PEG 3350 hung over a reservoir of 26% PEG 400.
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 20290 / Num. obs: 20290 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.09 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ARB

1arb


Resolution: 2.1→36.16 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.696 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22291 911 5.1 %RANDOM
Rwork0.1678 ---
obs0.17073 16856 87.46 %-
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: 37.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.19 Å2
2---0.41 Å20 Å2
3---0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.1→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 245 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192387
X-RAY DIFFRACTIONr_bond_other_d0.0070.022071
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.943261
X-RAY DIFFRACTIONr_angle_other_deg1.0833.0034794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4025329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54124.94693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4961512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212827
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02511
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7236 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 23 -
Rwork0.184 616 -
obs--42.86 %

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