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- PDB-1pxz: 1.7 Angstrom Crystal Structure of jun a 1, the major allergen fro... -

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Basic information

Entry
Database: PDB / ID: 1pxz
Title1.7 Angstrom Crystal Structure of jun a 1, the major allergen from cedar pollen
ComponentsMajor pollen allergen Jun a 1
KeywordsALLERGEN / parallel beta-helix / cedar pollen
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / metal ion binding
Similarity search - Function
AmbAllergen / Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesJuniperus ashei (Ozark white cedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsCzerwinski, E.W. / White, M.A. / Midoro-Horiuti, T. / Brooks, E.G. / Goldblum, R.M.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
Authors: Czerwinski, E.W. / Midoro-Horiuti, T. / White, M.A. / Brooks, E.G. / Goldblum, R.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray diffraction analysis of Jun a 1, the major allergen isolated from pollen of the mountain cedar Juniperus ashei
Authors: Liu, D. / Midoro-Horiuti, T. / White, M.A. / Brooks, E.G. / Goldblum, R.M. / Czerwinski, E.W.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major pollen allergen Jun a 1
B: Major pollen allergen Jun a 1


Theoretical massNumber of molelcules
Total (without water)75,3622
Polymers75,3622
Non-polymers00
Water12,629701
1
A: Major pollen allergen Jun a 1


Theoretical massNumber of molelcules
Total (without water)37,6811
Polymers37,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major pollen allergen Jun a 1


Theoretical massNumber of molelcules
Total (without water)37,6811
Polymers37,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.636, 115.005, 73.525
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major pollen allergen Jun a 1


Mass: 37680.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: pollen / Source: (natural) Juniperus ashei (Ozark white cedar) / References: UniProt: P81294
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, ammonium acetate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 89001 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3063 / Rsym value: 0.225 / % possible all: 47.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
SHELXL-97refinement
HKL-2000data reduction
RESOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→100 Å / Num. parameters: 24091 / Num. restraintsaints: 21849 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used conjugate gradient least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4446 5.3 %RANDOM
Rwork0.1925 ---
obs0.1931 89001 86.7 %-
all-84532 --
Displacement parametersBiso mean: 21.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.179 Å / Luzzati d res low obs: 6 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6022
Refinement stepCycle: LAST / Resolution: 1.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 0 701 5991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.077
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.7→1.74 Å
RfactorNum. reflection% reflection
Rwork0.224 --
obs-3063 44.8 %

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