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- PDB-4igy: Crystal structure of kirola (Act d 11) - triclinic form -

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Basic information

Entry
Database: PDB / ID: 4igy
TitleCrystal structure of kirola (Act d 11) - triclinic form
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 / MOLECULAR REPLACEMENT / Resolution: 2.92 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
B: Kirola
C: Kirola
D: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,72715
Polymers69,6924
Non-polymers3511
Water57632
1
A: Kirola


Theoretical massNumber of molelcules
Total (without water)17,4233
Polymers17,4231
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kirola


Theoretical massNumber of molelcules
Total (without water)17,4233
Polymers17,4231
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4585
Polymers17,4231
Non-polymers354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Kirola


Theoretical massNumber of molelcules
Total (without water)17,4234
Polymers17,4231
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.144, 56.094, 64.949
Angle α, β, γ (deg.)66.34, 85.37, 65.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 150
2111B1 - 150
3111C1 - 150
4111D1 - 150

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Components

#1: Protein
Kirola / Act d 11


Mass: 17422.963 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Actinidia deliciosa (kiwifruit) / References: UniProt: P85524
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M citric acid, 0.35 M magnesium 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: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. all: 14019 / Num. obs: 14019 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 8.3
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.1 / Num. unique all: 688 / Rsym value: 0.298 / % possible all: 94.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IGV

4igv


Resolution: 2.92→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25833 695 5 %RANDOM
Rwork0.20951 ---
all0.21186 13275 --
obs0.21186 13275 98.24 %-
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: 69.208 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20.73 Å22.36 Å2
2---1.26 Å2-1.1 Å2
3---3.9 Å2
Refinement stepCycle: LAST / Resolution: 2.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 11 32 4839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224888
X-RAY DIFFRACTIONr_bond_other_d00.023229
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9566607
X-RAY DIFFRACTIONr_angle_other_deg4.13637957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68925.789228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39815918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.347158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025303
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02945
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_it0.9531.52913
X-RAY DIFFRACTIONr_mcbond_other01.51202
X-RAY DIFFRACTIONr_mcangle_it1.8224774
X-RAY DIFFRACTIONr_scbond_it1.8531975
X-RAY DIFFRACTIONr_scangle_it3.4364.51833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1997 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.140.05
Btight positional0.150.05
Ctight positional0.140.05
Dtight positional0.150.05
Atight thermal0.070.5
Btight thermal0.060.5
Ctight thermal0.060.5
Dtight thermal0.060.5
LS refinement shellResolution: 2.92→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 44 -
Rwork0.324 937 -
obs--94.6 %
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)
12.7254-0.024-0.35542.9999-0.29752.25950.0076-0.1290.05760.21630.0195-0.11830.01480.062-0.02720.35160.1108-0.16580.2461-0.01380.0882-0.62-0.0360.271
22.41380.391-0.51533.0674-0.40961.94560.0439-0.01830.00170.21110.0428-0.1807-0.0247-0.0336-0.08660.34130.1245-0.12840.1897-0.04160.1621-32.155-22.717-3.867
33.2027-0.2119-0.41842.68280.15032.14160.04850.276-0.0651-0.044-0.05490.0072-0.0952-0.04790.00640.35430.1241-0.16690.2347-0.00650.0984-50.706-34.581-26.506
43.06360.3328-0.29232.0334-0.12272.16090.01470.3992-0.0199-0.2446-0.01040.01250.18930.0002-0.00420.42780.147-0.14020.2809-0.01030.1317-28.534-53.735-30.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B2 - 148
3X-RAY DIFFRACTION3C2 - 148
4X-RAY DIFFRACTION4D2 - 148

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