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- PDB-8wkh: Crystal structure of group 13 allergen from Blomia tropicalis -

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Basic information

Entry
Database: PDB / ID: 8wkh
TitleCrystal structure of group 13 allergen from Blomia tropicalis
ComponentsFatty acid-binding protein
KeywordsALLERGEN / BETA BARREL / HELIX
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesBlomia tropicalis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, K.L. / Gong, Y. / Cui, Y.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Immunobiological properties and structure analysis of group 13 allergen from Blomia tropicalis and its IgE-mediated cross-reactivity.
Authors: Zhou, Y. / Zhu, K. / Li, Q. / Zhou, D. / Ren, Y. / Liao, Y. / Cao, P. / Gong, Y. / Cui, Y.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1073
Polymers14,8791
Non-polymers2282
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.332, 46.752, 47.331
Angle α, β, γ (deg.)90.000, 96.120, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-360-

HOH

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Components

#1: Protein Fatty acid-binding protein /


Mass: 14878.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In the sequence, the first residue G is a expression tag.
Source: (gene. exp.) Blomia tropicalis (arthropod) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH7.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 8802 / % possible obs: 96.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 34.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 35.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 4 / Num. unique obs: 420 / CC1/2: 0.838 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.49 Å / SU ML: 0.1559 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 448 5.1 %
Rwork0.1753 8343 -
obs0.1774 8791 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 2→30.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 15 139 1197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711070
X-RAY DIFFRACTIONf_angle_d0.84951431
X-RAY DIFFRACTIONf_chiral_restr0.0537159
X-RAY DIFFRACTIONf_plane_restr0.007183
X-RAY DIFFRACTIONf_dihedral_angle_d16.2471412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.27911610.18982663X-RAY DIFFRACTION92.62
2.29-2.880.2591480.23162783X-RAY DIFFRACTION96.92
2.88-30.490.19051390.15452897X-RAY DIFFRACTION98.03
Refinement TLS params.Method: refined / Origin x: 12.7576 Å / Origin y: 19.9387 Å / Origin z: 12.8294 Å
111213212223313233
T0.2401 Å20.0064 Å20.013 Å2-0.2294 Å2-0.0062 Å2--0.2059 Å2
L2.8689 °20.5363 °20.5856 °2-2.7189 °20.3701 °2--2.4619 °2
S0.0364 Å °0.0478 Å °0.0436 Å °0.0004 Å °0.0448 Å °0.024 Å °-0.0747 Å °0.0033 Å °-0.0746 Å °

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