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- PDB-2j23: Cross-reactivity and crystal structure of Malassezia sympodialis ... -

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Basic information

Entry
Database: PDB / ID: 2j23
TitleCross-reactivity and crystal structure of Malassezia sympodialis Thioredoxin (Mala s 13), a member of a new pan-allergen family
ComponentsTHIOREDOXIN
KeywordsIMMUNE PROTEIN / MALASSEZIA SYMPODIALIS / AUTOREACTIVITY / CROSS-REACTIVITY / IGE / FUNGI / EPITOPE / ALLERGEN / THIOREDOXIN
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMALASSEZIA SYMPODIALIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsLimacher, A. / Glaser, A.G. / Meier, C. / Scapozza, L. / Crameri, R.
CitationJournal: J Immunol. / Year: 2007
Title: Cross-reactivity and 1.4-A crystal structure of Malassezia sympodialis thioredoxin (Mala s 13), a member of a new pan-allergen family.
Authors: Limacher, A. / Glaser, A.G. / Meier, C. / Schmid-Grendelmeier, P. / Zeller, S. / Scapozza, L. / Crameri, R.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)26,6782
Polymers26,6782
Non-polymers00
Water2,954164
1
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)13,3391
Polymers13,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)13,3391
Polymers13,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.496, 51.986, 53.023
Angle α, β, γ (deg.)90.00, 99.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99944, 0.03235, 0.00827), (0.03119, 0.99286, -0.11514), (-0.01193, -0.11482, -0.99331)
Vector: 33.60353, 1.23116, 26.10606)

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Components

#1: Protein THIOREDOXIN /


Mass: 13339.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MALASSEZIA SYMPODIALIS (fungus) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q1RQI9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growpH: 7
Details: 1.8 M AMMONIUM SULFATE, 3% PEG400, 0.1 M IMIDAZOLE PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00802
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00802 Å / Relative weight: 1
ReflectionResolution: 1.41→37 Å / Num. obs: 38712 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.9
Reflection shellResolution: 1.41→1.43 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EP7

1ep7


Resolution: 1.41→37 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.867 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1938 5 %RANDOM
Rwork0.14 ---
obs0.141 36757 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.08 Å2
2--0.32 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.41→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 0 164 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221898
X-RAY DIFFRACTIONr_bond_other_d0.0020.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9132579
X-RAY DIFFRACTIONr_angle_other_deg0.7833957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0255237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89925.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.83515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.231153
X-RAY DIFFRACTIONr_chiral_restr0.0610.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_nbd_refined0.2480.2331
X-RAY DIFFRACTIONr_nbd_other0.1680.21556
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2927
X-RAY DIFFRACTIONr_nbtor_other0.0850.2945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2671.51522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.99521939
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6643831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3724.5640
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 130
Rwork0.161 2606

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