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- PDB-3ft1: Crystal structure of pollen allergen Phl p 3 -

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Basic information

Entry
Database: PDB / ID: 3ft1
TitleCrystal structure of pollen allergen Phl p 3
ComponentsPhl p 3 allergen
KeywordsALLERGEN / BETA-BARREL
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Pollen allergen Lol p2 / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / Expansin, cellulose-binding-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKeller, W. / Devanaboyina, S.C.
CitationJournal: Allergy / Year: 2014
Title: High-resolution crystal structure and IgE recognition of the major grass pollen allergen Phl p 3.
Authors: Devanaboyina, S.C. / Cornelius, C. / Lupinek, C. / Fauland, K. / Dall'Antonia, F. / Nandy, A. / Hagen, S. / Flicker, S. / Valenta, R. / Keller, W.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 12, 2023Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phl p 3 allergen
B: Phl p 3 allergen
C: Phl p 3 allergen
D: Phl p 3 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,87014
Polymers45,5164
Non-polymers35510
Water10,287571
1
A: Phl p 3 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4854
Polymers11,3791
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phl p 3 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4854
Polymers11,3791
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phl p 3 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4503
Polymers11,3791
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phl p 3 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4503
Polymers11,3791
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.068, 74.447, 56.693
Angle α, β, γ (deg.)90.00, 104.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phl p 3 allergen


Mass: 11378.952 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Production host: Escherichia coli (E. coli) / References: UniProt: Q69B42
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1 M Bis-tris, 0.1 M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8148 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2007
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.79→30 Å / Num. all: 34582 / Num. obs: 34582 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 149.7
Reflection shellHighest resolution: 1.79 Å

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WHO

1who


Resolution: 1.79→30 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1730 -RANDOM
Rwork0.17 ---
obs0.17 34582 99.8 %-
all-34582 --
Displacement parametersBiso mean: 18.3 Å2
Refinement stepCycle: LAST / Resolution: 1.79→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 10 571 3796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.55
X-RAY DIFFRACTIONp_bond_d0.014
LS refinement shellHighest resolution: 1.79 Å / Num. reflection obs: 206729

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