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

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Basic information

Entry
Database: PDB / ID: 4igx
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: 2.35 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 ...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

Downloads & links

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Assembly

Deposited unit
A: Kirola
B: Kirola
C: Kirola
D: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,82514
Polymers69,6924
Non-polymers13310
Water1,09961
1
A: Kirola


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


Theoretical massNumber of molelcules
Total (without water)17,4584
Polymers17,4231
Non-polymers353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
4
D: Kirola
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4852
Polymers17,4231
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.661, 43.039, 94.126
Angle α, β, γ (deg.)76.70, 85.67, 83.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 5 / Auth seq-ID: 5 - 146 / Label seq-ID: 5 - 146

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M sodium chloride, 25% 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 23741 / Num. obs: 23741 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 18.3
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1058 / Rsym value: 0.34 / % possible all: 84.8

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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: 2.35→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.684 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.497 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1215 5.1 %RANDOM
Rwork0.1839 ---
all0.18695 22488 --
obs0.18695 22488 97.12 %-
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: 77.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.24 Å2-0.51 Å2
2--2.68 Å22.67 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 13 61 4677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224699
X-RAY DIFFRACTIONr_bond_other_d00.023048
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9566365
X-RAY DIFFRACTIONr_angle_other_deg4.24537507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57225.604207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4715843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.846158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025111
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02921
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_it0.5221.52854
X-RAY DIFFRACTIONr_mcbond_other01.51175
X-RAY DIFFRACTIONr_mcangle_it0.99724658
X-RAY DIFFRACTIONr_scbond_it1.69231845
X-RAY DIFFRACTIONr_scangle_it2.7684.51707
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 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A818medium positional0.180.5
B818medium positional0.240.5
C818medium positional0.270.5
D818medium positional0.190.5
A958loose positional0.465
B958loose positional0.445
C958loose positional0.55
D958loose positional0.455
A818medium thermal0.452
B818medium thermal0.512
C818medium thermal0.392
D818medium thermal0.422
A958loose thermal0.6710
B958loose thermal0.6910
C958loose thermal0.5910
D958loose thermal0.5510
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 73 -
Rwork0.229 1491 -
obs--86.17 %
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)
13.7925-0.3145-1.33871.7665-0.60956.4438-0.04630.1238-0.24720.03420.1176-0.01320.2063-0.3821-0.07130.17680.0194-0.00620.0327-0.0030.2567-2.104-6.3560.911
23.05530.07291.27472.62930.39223.0064-0.0301-0.07060.15220.0915-0.0446-0.0376-0.193-0.12060.07470.16330.02620.01830.0536-0.02210.2052-2.8755.0240.049
33.13811.81590.09096.0388-4.21714.55330.19180.0555-0.01320.1153-0.2287-0.23920.03740.56780.03690.21710.02640.0390.1664-0.06670.30566.507-2.193-1.172
45.8959-1.20051.45372.1798-0.66814.73730.1148-0.02340.3082-0.01060.08120.1393-0.2289-0.4164-0.1960.1904-0.00960.03260.08950.04670.2483-21.56-11.01914.795
53.7986-1.22310.12824.07230.03842.43230.0850.0066-0.2585-0.19680.07980.23040.2501-0.1035-0.16480.207-0.009-0.02380.0323-0.01790.2326-21.507-21.93716.77
64.1572-1.49181.21295.8689-3.14473.55180.3573-0.06470.1413-0.0911-0.357-0.15610.12770.742-0.00030.2350.01880.01050.2078-0.04660.2893-12.158-15.98617.319
73.69811.1497-2.68913.94341.11947.2145-0.00280.37190.3576-0.2590.26880.3296-0.8185-0.2888-0.2660.52450.02650.00610.22050.05980.2841-17.1957.711-24.478
82.08221.08-0.35484.30880.98357.306-0.08840.3361-0.001-0.47770.02630.21780.2228-0.48260.06210.27730.0116-0.00410.14730.00360.2048-18.868-2.501-21.712
92.4854-0.6166-0.527515.168-0.05176.7914-0.16670.229-0.0437-0.85580.17610.1981-0.09510.0452-0.00940.5066-0.06870.0970.2382-0.03910.2497-13.2770.986-31.402
103.8670.0664-0.43494.38770.62636.3473-0.01040.1472-0.14910.54150.0226-0.19790.4365-0.0336-0.01220.4207-0.078-0.06860.18150.02690.2206-36.586-21.82641.513
112.7951-0.70470.02952.93370.21253.61170.08770.05280.24290.4779-0.1709-0.0865-0.3122-0.1140.08320.3342-0.0628-0.00490.1422-0.00480.2456-38.086-11.16937.663
123.18020.3580.16427.482-2.155.70010.0233-0.05410.05381.20660.024-0.0041-0.06270.2627-0.04740.5593-0.015-0.13210.3483-0.0410.355-31.86-15.52446.888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 42
2X-RAY DIFFRACTION2A43 - 106
3X-RAY DIFFRACTION3A107 - 149
4X-RAY DIFFRACTION4B3 - 43
5X-RAY DIFFRACTION5B44 - 106
6X-RAY DIFFRACTION6B107 - 148
7X-RAY DIFFRACTION7C3 - 42
8X-RAY DIFFRACTION8C43 - 106
9X-RAY DIFFRACTION9C107 - 147
10X-RAY DIFFRACTION10D3 - 43
11X-RAY DIFFRACTION11D44 - 103
12X-RAY DIFFRACTION12D104 - 148

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