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- PDB-3v0r: Crystal structure of Alternaria alternata allergen Alt a 1 -

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Basic information

Entry
Database: PDB / ID: 3v0r
TitleCrystal structure of Alternaria alternata allergen Alt a 1
ComponentsMajor allergen Alt a 1
KeywordsUNKNOWN FUNCTION / beta-barrel / cell wall
Function / homology
Function and homology information


ascospore wall / extracellular region
Similarity search - Function
AOC barrel-like - #20 / Alternaria alternata allergen 1 / Alternaria alternata allergen 1 / Alt a 1 (AA1)-like domain profile. / AOC barrel-like / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2,5,6-triaminopyrimidin-4-ol / 8-aminooctanoic acid / Major allergen Alt a 1
Similarity search - Component
Biological speciesAlternaria alternata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChruszcz, M. / Solberg, R. / Osinski, T. / Chapman, M.D. / Minor, W.
CitationJournal: J.Allergy Clin.Immunol. / Year: 2012
Title: Alternaria alternata allergen Alt a 1: a unique beta-barrel protein dimer found exclusively in fungi.
Authors: Chruszcz, M. / Chapman, M.D. / Osinski, T. / Solberg, R. / Demas, M. / Porebski, P.J. / Majorek, K.A. / Pomes, A. / Minor, W.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major allergen Alt a 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,57213
Polymers14,6051
Non-polymers96712
Water2,828157
1
A: Major allergen Alt a 1
hetero molecules

A: Major allergen Alt a 1
hetero molecules

A: Major allergen Alt a 1
hetero molecules

A: Major allergen Alt a 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28852
Polymers58,4214
Non-polymers3,86748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area9660 Å2
ΔGint-182 kcal/mol
Surface area25380 Å2
MethodPISA
2
A: Major allergen Alt a 1
hetero molecules

A: Major allergen Alt a 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14426
Polymers29,2102
Non-polymers1,93424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area3950 Å2
ΔGint-104 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.016, 70.016, 179.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-208-

UNX

21A-209-

0FU

31A-209-

0FU

41A-210-

0FU

51A-452-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Major allergen Alt a 1


Mass: 14605.165 Da / Num. of mol.: 1 / Fragment: UNP residues 26-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alternaria alternata (fungus) / Gene: ALTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P79085

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Non-polymers , 5 types, 169 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-0FU / 2,5,6-triaminopyrimidin-4-ol / 4-hydroxy-2,5,6-triaminopyrimidine


Mass: 141.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7N5O
#5: Chemical ChemComp-8AC / 8-aminooctanoic acid / 8-aminocaprylic acid


Mass: 159.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50% saturated ammonium sulfate, 12.5% of additive mixture (saturated solution of 4-hydroxy-2,5,5-triaminopyrimidine, alpha-lipoic acid, caffeine, 8-aminocaprylic acid, threonine, carnitine ...Details: 50% saturated ammonium sulfate, 12.5% of additive mixture (saturated solution of 4-hydroxy-2,5,5-triaminopyrimidine, alpha-lipoic acid, caffeine, 8-aminocaprylic acid, threonine, carnitine and quinine HCl), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.979
SYNCHROTRONAPS 21-ID-G20.9786
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDJul 6, 2011
MARMOSAIC 300 mm CCD2CCDOct 20, 2011
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97861
ReflectionResolution: 1.9→50 Å / Num. all: 18157 / Num. obs: 18157 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 59.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 4.2 / Num. unique all: 878 / Rsym value: 0.777 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MD2data collection
HKL-3000SHELXC/D/Ephasing
MLPHAREphasing
DMmodel building
PARROTphasing
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.6.0117refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.475 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 923 5.1 %RANDOM
Rwork0.16707 ---
all0.16815 17140 --
obs0.16815 17140 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 65 157 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021100
X-RAY DIFFRACTIONr_bond_other_d0.0270.02701
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9921501
X-RAY DIFFRACTIONr_angle_other_deg0.973.0121703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49824.68147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.606153
X-RAY DIFFRACTIONr_chiral_restr0.1230.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 68 -
Rwork0.246 1109 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6932-10.82350.541835.3296-5.1511.20330.0390.09-0.5159-0.4180.14531.43170.0986-0.0853-0.18430.1994-0.0148-0.03860.1170.01920.205617.22912.99319.066
21.34661.04641.3072.6723.14735.71770.0813-0.1462-0.04890.2411-0.0214-0.07620.2143-0.1046-0.060.1680.0176-0.00450.03440.020.104428.70212.0336.735
30.76990.2703-0.61970.2854-0.00141.7713-0.041-0.07410.02350.080.038-0.0480.00560.04160.00310.18520.0285-0.01160.05210.00040.126932.22715.60732.905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 36
2X-RAY DIFFRACTION2A37 - 81
3X-RAY DIFFRACTION3A82 - 156

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