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- PDB-4igw: Crystal structure of kirola (Act d 11) in P6122 space group -

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Basic information

Entry
Database: PDB / ID: 4igw
TitleCrystal structure of kirola (Act d 11) in P6122 space group
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 / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / pdbx_struct_special_symmetry / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Kirola
B: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,04111
Polymers34,8462
Non-polymers1959
Water1,00956
1
A: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5206
Polymers17,4231
Non-polymers985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5205
Polymers17,4231
Non-polymers984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.989, 59.989, 339.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-204-

CL

21B-203-

CL

31A-306-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 2 - 148 / Label seq-ID: 2 - 148

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

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Components

#1: Protein Kirola / Act d 11


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


Num. of mol.: 5 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M sodium chloride, 25% w/v PEG3350, 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: 2.55→50 Å / Num. all: 12244 / Num. obs: 12244 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 21.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.4 / Num. unique all: 602 / Rsym value: 0.61 / % possible all: 95.3

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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: 2.55→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 25.064 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.688 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25299 597 4.9 %RANDOM
Rwork0.21802 ---
all0.21973 11621 --
obs0.21973 11621 95.32 %-
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: 55.764 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å2-2.02 Å20 Å2
2---4.03 Å20 Å2
3---6.05 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 15 56 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222455
X-RAY DIFFRACTIONr_bond_other_d0.0130.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9583313
X-RAY DIFFRACTIONr_angle_other_deg1.21934019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24425.789114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.85154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022655
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02473
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_it0.7431.51459
X-RAY DIFFRACTIONr_mcbond_other0.1551.5602
X-RAY DIFFRACTIONr_mcangle_it1.36222391
X-RAY DIFFRACTIONr_scbond_it1.8083996
X-RAY DIFFRACTIONr_scangle_it2.9554.5922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2009 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.220.5
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 37 -
Rwork0.31 853 -
obs--95.6 %
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)
13.89190.5495-0.19983.164-0.16891.37470.0467-0.47090.17740.1734-0.0491-0.19480.03280.08670.00240.08090.0065-0.00870.4709-0.1130.043821.464-0.28415.71
23.1892-0.4118-0.12521.6729-0.34162.0076-0.0634-0.37610.45370.11750.184-0.1081-0.0172-0.2252-0.12060.08780.0071-0.00930.443-0.10450.0824-6.3138.77812.972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2B1 - 148

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