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- PDB-7ksc: Crystal structure of Pun g 1.0101 -

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Basic information

Entry
Database: PDB / ID: 7ksc
TitleCrystal structure of Pun g 1.0101
ComponentsNon-specific lipid-transfer protein
KeywordsALLERGEN / nsLTP / food allergen
Function / homologyPlant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / lipid transport / lipid binding / Non-specific lipid-transfer protein
Function and homology information
Biological speciesPunica granatum (pomegranate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPote, S. / O'Malley, A. / Gawlicka-Chruszcz, A. / Tuppo, L. / Ciardiello, M.A. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077653 United States
CitationJournal: Molecules / Year: 2021
Title: Structural Characterization of Act c 10.0101 and Pun g 1.0101-Allergens from the Non-Specific Lipid Transfer Protein Family.
Authors: O'Malley, A. / Pote, S. / Giangrieco, I. / Tuppo, L. / Gawlicka-Chruszcz, A. / Kowal, K. / Ciardiello, M.A. / Chruszcz, M.
History
DepositionNov 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Non-specific lipid-transfer protein
B: Non-specific lipid-transfer protein
C: Non-specific lipid-transfer protein
D: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30413
Polymers37,4404
Non-polymers8659
Water84747
1
A: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4562
Polymers9,3601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5523
Polymers9,3601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6484
Polymers9,3601
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6484
Polymers9,3601
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Non-specific lipid-transfer protein
C: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1046
Polymers18,7202
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-52 kcal/mol
Surface area10100 Å2
MethodPISA
6
B: Non-specific lipid-transfer protein
D: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2007
Polymers18,7202
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-63 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.522, 89.424, 58.940
Angle α, β, γ (deg.)90.000, 102.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 93 / Label seq-ID: 1 - 93

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Non-specific lipid-transfer protein


Mass: 9359.901 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Punica granatum (pomegranate) / Gene: CRG98_038474 / Production host: unidentified (others) / References: UniProt: A0A059STC4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6 and 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10593 / % possible obs: 90.6 % / Redundancy: 2.8 % / Rpim(I) all: 0.124 / Rrim(I) all: 0.22 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 548 / CC1/2: 0.751 / Rpim(I) all: 0.316 / Rrim(I) all: 0.511 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TVI

5tvi


Resolution: 2.4→35.32 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 23.831 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 541 5.1 %RANDOM
Rwork0.2038 ---
obs0.2064 10014 90.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.65 Å2 / Biso mean: 33.686 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20.11 Å2
2---1.69 Å2-0 Å2
3---3.16 Å2
Refinement stepCycle: final / Resolution: 2.4→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 45 47 2672
Biso mean--61.11 35.64 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132672
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172520
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.6543654
X-RAY DIFFRACTIONr_angle_other_deg2.3371.5745882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7885368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.55519.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0781516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022944
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02464
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A25190.09
12B25190.09
21A24340.14
22C24340.14
31A24450.13
32D24450.13
41B24170.15
42C24170.15
51B24210.14
52D24210.14
61C25530.1
62D25530.1
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 32 -
Rwork0.233 728 -
all-760 -
obs--85.01 %
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)
13.34050.4730.90430.91790.30061.31520.04090.00180.1752-0.0222-0.06480.1710.14480.08390.02390.0255-0.0089-0.01860.1470.00040.14541.27-15.45533.495
23.55245.7075-3.766112.2608-3.62755.9109-0.1064-0.0139-0.0110.00660.09050.00080.28230.04050.01590.0261-0.0143-0.0260.18730.02950.07769.875-18.50535.865
33.78183.78921.19255.1441-1.89148.61240.07340.04950.18560.072-0.09760.09510.14670.11320.02410.07690.047-0.06510.14080.00950.10353.72-27.75528.909
44.01470.3460.5390.56090.5331.39160.0554-0.2267-0.0025-0.0615-0.0371-0.05680.01130.0114-0.01820.0194-0.0084-0.0070.10820.00720.0703-7.174-18.3746.517
57.06192.30251.82680.95131.34163.3027-0.125-0.0877-0.0444-0.06350.04910.0169-0.07220.38820.07590.09680.036-0.02630.17120.02020.10892.241-19.9192.527
62.95582.06430.27722.41572.28199.5791-0.05-0.0615-0.06350.0012-0.0639-0.12170.0129-0.09360.11390.01460.03990.00120.13890.04620.1306-4.54-29.4263.542
71.1027-0.3594-0.22420.17380.14881.81050.0651-0.1607-0.0636-0.02580.06470.06670.0325-0.0384-0.12980.027-0.0388-0.02350.18690.0140.09759.6391.52328.87
82.82673.22670.37317.00130.96830.6692-0.00360.2248-0.348-0.0499-0.01190.19840.1387-0.14860.01550.05720.0068-0.03330.2558-0.05460.19972.5116.03826.748
99.96482.20032.15732.56881.54824.60830.0394-0.32150.56110.3784-0.36770.3854-0.0588-0.57840.32840.1225-0.0156-0.00750.2425-0.03380.14757.387.01215.443
103.0625-0.5497-0.40930.95050.65771.4450.0749-0.2228-0.07160.0182-0.0277-0.0412-0.0480.0896-0.04720.0437-0.001-0.03380.21780.01540.1151.951-0.8821.72
112.96951.7154-1.13092.7906-1.53020.8580.11610.1084-0.16470.0449-0.1389-0.0122-0.03280.05810.02280.01980.0284-0.04540.2299-0.01750.1253-5.4761.24-1.271
128.01156.74315.91767.62080.922713.1028-0.0266-0.26580.55110.1099-0.11350.5934-0.3795-0.71180.14010.04320.0998-0.00650.3153-0.01570.1446-0.6035.143-12.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 58
2X-RAY DIFFRACTION2A59 - 78
3X-RAY DIFFRACTION3A79 - 93
4X-RAY DIFFRACTION4B1 - 53
5X-RAY DIFFRACTION5B54 - 73
6X-RAY DIFFRACTION6B74 - 93
7X-RAY DIFFRACTION7C1 - 56
8X-RAY DIFFRACTION8C57 - 82
9X-RAY DIFFRACTION9C83 - 93
10X-RAY DIFFRACTION10D1 - 52
11X-RAY DIFFRACTION11D53 - 80
12X-RAY DIFFRACTION12D81 - 93

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