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- PDB-4ih2: Crystal structure of kirola (Act d 11) from crystal soaked with 2... -

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Basic information

Entry
Database: PDB / ID: 4ih2
TitleCrystal structure of kirola (Act d 11) from crystal soaked with 2-aminopurine
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 (Chinese gooseberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 1.1Apr 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 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4583
Polymers17,4231
Non-polymers352
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.592, 71.592, 114.446
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-201-

CL

21A-376-

HOH

31A-387-

HOH

41A-389-

HOH

51A-390-

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 (Chinese gooseberry) / References: UniProt: P85524
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M citric acid, 0.3 M magnesium chloride, 0.01 M calcium chloride, pH 5.5, 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 22, 2010
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: 2→50 Å / Num. all: 12396 / Num. obs: 12396 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 44.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 5.8 / Num. unique all: 590 / Rsym value: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4IGV

4igv


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.481 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24423 594 4.8 %RANDOM
Rwork0.1973 ---
obs0.19943 11691 99.55 %-
all-11691 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.928 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å21.43 Å20 Å2
2--2.86 Å20 Å2
3----4.3 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 11 98 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021220
X-RAY DIFFRACTIONr_bond_other_d0.010.02795
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9671651
X-RAY DIFFRACTIONr_angle_other_deg1.05331957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86225.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78815222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.636152
X-RAY DIFFRACTIONr_chiral_restr0.120.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 34 -
Rwork0.217 728 -
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)
115.73619.9837-11.351810.3346-8.973513.3954-0.5348-0.0056-0.3441-0.21370.0532-0.72070.95350.46180.48160.15420.0912-0.07570.27480.03150.2165-9.727-31.496-14.353
20.12510.3341-0.48382.2649-1.06782.10290.0294-0.0105-0.02560.0855-0.06310.0714-0.1769-0.06470.03360.05720.0353-0.0190.08220.01660.1284-24.854-20.925-13.797
30.52040.18410.64464.96550.91474.72060.07690.0305-0.032-0.0003-0.1581-0.1582-0.05070.16960.08120.02340.0122-0.03050.11680.0250.1209-18.235-21.99-18.214
41.9960.87940.08444.63110.24513.10150.1630.1082-0.00720.0998-0.2888-0.14870.02640.46270.12590.02830.0139-0.03550.16810.05350.1099-13.01-22.535-18.797
52.35720.8008-1.41021.7909-1.86743.82310.1254-0.0430.0550.1861-0.1985-0.1701-0.08580.49630.07320.03990.0125-0.0420.15810.05380.1321-11.103-25.225-11.219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 62
3X-RAY DIFFRACTION3A63 - 84
4X-RAY DIFFRACTION4A85 - 111
5X-RAY DIFFRACTION5A112 - 149

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