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- PDB-2p9w: Crystal Structure of the Major Malassezia sympodialis Allergen Ma... -

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Basic information

Entry
Database: PDB / ID: 2p9w
TitleCrystal Structure of the Major Malassezia sympodialis Allergen Mala s 1
ComponentsMal s 1 allergenic protein
KeywordsALLERGEN / beta propeller
Function / homology: / Mal s 1 allergenic protein-like / Mal s 1 allergenic protein
Function and homology information
Biological speciesMalassezia sympodialis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsVilhelmsson, M. / Zargari, A. / Crameri, R. / Rasool, O. / Achour, A. / Scheynius, A. / Hallberg, B.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Major Malassezia sympodialis Allergen Mala s 1 Reveals a beta-Propeller Fold: A Novel Fold Among Allergens.
Authors: Vilhelmsson, M. / Zargari, A. / Crameri, R. / Rasool, O. / Achour, A. / Scheynius, A. / Hallberg, B.M.
History
DepositionMar 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE There was no UNP sequence reference available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mal s 1 allergenic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,66710
Polymers36,8751
Non-polymers7929
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.480, 164.000, 50.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Mal s 1 allergenic protein


Mass: 36874.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malassezia sympodialis (fungus) / Gene: Mala s1 / Plasmid: PET-21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6WIF3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 8K, 0.2 M (NH4)2SO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2006
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 91792 / Num. obs: 91336 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.101 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.353.50.60889760.996199.2
1.35-1.43.60.48790021.041199.9
1.4-1.463.60.35890351.034199.8
1.46-1.543.60.26890681.061199.7
1.54-1.643.60.19490771.09199.8
1.64-1.763.60.13891001.094199.7
1.76-1.943.60.09791061.06199.4
1.94-2.223.60.06891481.028199.4
2.22-2.83.60.05192091.078199.2
2.8-5010.80.05596151.208199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→44.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 1646 2 %RANDOM
Rwork0.139 ---
obs0.139 82044 99.41 %-
all-82536 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 44 396 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212983
X-RAY DIFFRACTIONr_bond_other_d00.022016
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.944080
X-RAY DIFFRACTIONr_angle_other_deg4.23234921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73724.521146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69615479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2471515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023533
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02637
X-RAY DIFFRACTIONr_nbd_refined0.2080.2514
X-RAY DIFFRACTIONr_nbd_other0.2390.22106
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21429
X-RAY DIFFRACTIONr_nbtor_other0.1150.21436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.224
X-RAY DIFFRACTIONr_mcbond_it3.39521836
X-RAY DIFFRACTIONr_mcbond_other3.4632740
X-RAY DIFFRACTIONr_mcangle_it4.30232988
X-RAY DIFFRACTIONr_scbond_it4.55621147
X-RAY DIFFRACTIONr_scangle_it6.06431092
X-RAY DIFFRACTIONr_rigid_bond_restr3.52134999
X-RAY DIFFRACTIONr_sphericity_free14.8623397
X-RAY DIFFRACTIONr_sphericity_bonded5.62334908
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 117 -
Rwork0.217 5852 -
obs-5969 99.68 %

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