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- PDB-7ksb: Crystal structure on Act c 10.0101 -

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Basic information

Entry
Database: PDB / ID: 7ksb
TitleCrystal structure on Act c 10.0101
ComponentsNon-specific lipid-transfer protein 1
KeywordsALLERGEN / nsLTP / food allergen
Function / homologyPlant 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 / membrane / Non-specific lipid-transfer protein 1
Function and homology information
Biological speciesActinidia chinensis var. chinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPote, S. / O'Malley, A. / Gawlicka-Chruszcz, A. / Giangrieco, I. / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific lipid-transfer protein 1
B: Non-specific lipid-transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5228
Polymers18,9462
Non-polymers5766
Water1,49583
1
A: Non-specific lipid-transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7614
Polymers9,4731
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-specific lipid-transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7614
Polymers9,4731
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-64 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.812, 38.130, 48.414
Angle α, β, γ (deg.)90.000, 98.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 92 / Label seq-ID: 1 - 92

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

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Components

#1: Protein Non-specific lipid-transfer protein 1 / LTP1


Mass: 9472.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Actinidia chinensis var. chinensis (plant)
References: UniProt: P85204
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4
Details: 0.1 M citric acid buffer, pH 4.0 with 3.0 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: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 10217 / % possible obs: 98.7 % / Redundancy: 4 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.113 / Net I/σ(I): 25.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 497 / CC1/2: 0.904 / Rpim(I) all: 0.24 / Rrim(I) all: 0.483 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZL

1rzl


Resolution: 1.95→27.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.241 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 503 4.9 %RANDOM
Rwork0.1993 ---
obs0.2021 9707 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.19 Å2 / Biso mean: 26.802 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å2-3.07 Å2
2---0.73 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.95→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 30 83 1419
Biso mean--54.35 31.01 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131361
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181309
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.6521846
X-RAY DIFFRACTIONr_angle_other_deg1.5691.593034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1812245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.907158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
Refine LS restraints NCS

Ens-ID: 1 / Number: 2528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 24 -
Rwork0.223 666 -
all-690 -
obs--92.74 %
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)
10.60480.37750.03370.2798-0.3192.69060.02260.071-0.0117-0.00020.04940.00050.10140.0501-0.07190.04010.0080.04140.0724-0.00990.06035.5391.566.078
24.32980.7646-1.01790.58460.2771.8562-0.14820.013-0.2750.08190.0854-0.01680.28610.21490.06280.06790.05280.02760.0760.00860.03278.11-6.5414.638
32.2709-0.09460.92070.36850.36410.8248-0.0630.0103-0.0351-0.06650.0846-0.0104-0.09730.0754-0.02160.05-0.01930.04650.0849-0.00070.054912.10217.85316.899
43.7035-0.7755-3.23914.7741-2.06694.50780.43430.26810.3884-0.00360.12510.2036-0.4251-0.4203-0.55930.05760.01030.04420.19240.11250.121616.84225.23810.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION2A72 - 92
3X-RAY DIFFRACTION3B1 - 77
4X-RAY DIFFRACTION4B78 - 91

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