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- PDB-3ft9: X-ray Crystal structure of pollen allergen - Phl p 3 -

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Basic information

Entry
Database: PDB / ID: 3ft9
TitleX-ray Crystal 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 12, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phl p 3 allergen


Theoretical massNumber of molelcules
Total (without water)11,3791
Polymers11,3791
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.671, 46.767, 36.909
Angle α, β, γ (deg.)90.00, 91.99, 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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.87 Å3/Da / Density % sol: 34.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 3350, 0.1 M Bis-tris, 0.1 M NaCl, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→36.89 Å / Num. obs: 5096 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16222.7
Reflection shellResolution: 2.05→2.099 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 19.45 / Num. unique all: 13550 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.389 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22844 242 4.5 %RANDOM
Rwork0.16941 ---
obs0.17222 5096 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.42 Å2
2---0.58 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 0 81 831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022769
X-RAY DIFFRACTIONr_angle_refined_deg2.4091.9691037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.833593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.14124.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.24615141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.423154
X-RAY DIFFRACTIONr_chiral_restr0.1710.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021572
X-RAY DIFFRACTIONr_mcbond_it1.5361.5468
X-RAY DIFFRACTIONr_mcangle_it2.7622763
X-RAY DIFFRACTIONr_scbond_it4.233301
X-RAY DIFFRACTIONr_scangle_it6.8534.5274
LS refinement shellResolution: 2.05→2.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 14 -
Rwork0.22 364 -
obs--98.69 %

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