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- PDB-1whp: ALLERGEN PHL P 2 -

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Basic information

Entry
Database: PDB / ID: 1whp
TitleALLERGEN PHL P 2
ComponentsALLERGEN PHL P 2
KeywordsALLERGEN / TIMOTHY GRASS POLLEN ALLERGEN
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
Pollen allergen Phl p 2
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 3 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Dolecek, C. / Susani, M. / Valenta, R. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal Structure of Phl P 2, a Major Timothy Grass (Phleum Pratense) Pollen Allergen
Authors: Fedorov, A.A. / Fedorov, E.V. / Dolecek, C. / Susani, M. / Valenta, R. / Almo, S.C.
#1: Journal: FEBS Lett. / Year: 1993
Title: Molecular Characterization of Phl P II, a Major Timothy Grass (Phleum Pratense) Pollen Allergen
Authors: Dolecek, C. / Vrtala, S. / Laffer, S. / Steinberger, P. / Kraft, D. / Scheiner, O. / Valenta, R.
History
DepositionApr 4, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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: ALLERGEN PHL P 2


Theoretical massNumber of molelcules
Total (without water)10,8281
Polymers10,8281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.439, 39.439, 121.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ALLERGEN PHL P 2 / PHL P II


Mass: 10828.056 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: P43214

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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: 2.25 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.6 / Details: CRYSTALLIZED FROM 24% PEG 4000 SOLUTION., pH 4.6

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→24.1 Å / Num. obs: 2177 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1WHO

1who


Resolution: 3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.192 --
obs-1963 93.9 %
Displacement parametersBiso mean: 14.2 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 0 0 745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.018
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5361.5
X-RAY DIFFRACTIONp_mcangle_it2.7682
X-RAY DIFFRACTIONp_scbond_it2.2382
X-RAY DIFFRACTIONp_scangle_it3.813
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1150.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2690.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_planar_tor1.22
X-RAY DIFFRACTIONp_staggered_tor16.210
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor11.510
X-RAY DIFFRACTIONp_special_tor
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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