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- PDB-4igv: Crystal structure of kirola (Act d 11) -

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Basic information

Entry
Database: PDB / ID: 4igv
TitleCrystal structure of kirola (Act d 11)
ComponentsKirola
KeywordsALLERGEN / MLP/RRP family / PR-10 related
Function / homology
Function and homology information


activation of immune response / defense response
Similarity search - Function
: / Pathogenesis-related protein Bet v I family / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Kirola
Similarity search - Component
Biological speciesActinidia deliciosa (kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsChruszcz, M. / Ciardiello, M.A. / Giangrieco, I. / Osinski, T. / Minor, W.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Structural and bioinformatic analysis of the kiwifruit allergen Act d 11, a member of the family of ripening-related proteins.
Authors: Chruszcz, M. / Ciardiello, M.A. / Osinski, T. / Majorek, K.A. / Giangrieco, I. / Font, J. / Breiteneder, H. / Thalassinos, K. / Minor, W.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,52911
Polymers17,4231
Non-polymers10610
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.781, 71.781, 113.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

21A-367-

HOH

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Components

#1: Protein Kirola / Act d 11


Mass: 17422.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinidia deliciosa (kiwifruit) / References: UniProt: P85524
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 7 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.1 M Bis-Tris, 0.2 M magnesium chloride, 0.5% deoxycholate, 24% w/v PEG3350, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 28517 / Num. obs: 28517 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 30.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1380 / Rsym value: 0.538 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.298 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20336 1437 5 %RANDOM
Rwork0.16943 ---
all0.17112 27027 --
obs0.17112 27027 99.95 %-
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: 24.127 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 10 177 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221320
X-RAY DIFFRACTIONr_bond_other_d0.0020.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9611798
X-RAY DIFFRACTIONr_angle_other_deg2.29232142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03625.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42315250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12152
X-RAY DIFFRACTIONr_chiral_restr0.110.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021476
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02256
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_it1.0761.5796
X-RAY DIFFRACTIONr_mcbond_other0.1411.5324
X-RAY DIFFRACTIONr_mcangle_it1.95821318
X-RAY DIFFRACTIONr_scbond_it3.0063524
X-RAY DIFFRACTIONr_scangle_it4.8624.5480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 110 -
Rwork0.207 1937 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
114.8986-11.8707-10.015113.550810.03799.9752-0.01840.1172-0.34460.1998-0.40360.71750.4305-0.56360.4220.1425-0.0617-0.03070.2883-0.06930.158844.08731.11314.694
22.52950.7915-0.17322.7171-0.49521.7013-0.04830.1084-0.0571-0.0775-0.0244-0.03460.03410.00840.07270.11210.0005-0.00850.1559-0.00190.050963.43833.38213.957
30.77360.0159-0.83121.68270.6010.98250.0386-0.0003-0.0312-0.0376-0.1156-0.0072-0.12310.02860.0770.149-0.0297-0.02980.15020.00410.053261.39144.15713.53
43.1534-1.08243.43573.4499-0.616911.15270.0430.0324-0.0634-0.2915-0.11620.3077-0.4564-0.23210.07320.17610.0301-0.04470.1363-0.02850.061352.1649.28810.859
51.6182-2.37160.3425.9406-1.56322.6982-0.0148-0.0645-0.04690.1946-0.00550.2263-0.0284-0.08690.02030.0989-0.0263-0.0170.1556-0.01210.038254.52137.78222.725
62.6394-2.1733-0.68815.28471.44182.73360.0988-0.0279-0.0396-0.018-0.2230.36810.022-0.34730.12420.0613-0.0178-0.0180.2007-0.05340.061445.05437.65617.503
76.8639-1.8287-2.40832.38761.82234.7970.05880.14130.0516-0.2172-0.10760.0202-0.1601-0.14650.04890.13730.0043-0.02640.1485-0.02170.039651.79935.5255.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 30
3X-RAY DIFFRACTION3A31 - 55
4X-RAY DIFFRACTION4A56 - 71
5X-RAY DIFFRACTION5A72 - 91
6X-RAY DIFFRACTION6A92 - 128
7X-RAY DIFFRACTION7A129 - 150

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