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- PDB-2jmh: NMR solution structure of Blo t 5, a major mite allergen from Blo... -

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Basic information

Entry
Database: PDB / ID: 2jmh
TitleNMR solution structure of Blo t 5, a major mite allergen from Blomia tropicalis
ComponentsMite allergen Blo t 5
KeywordsALLERGEN / Dust mites / Blomia tropicalis / blo t 5 / Group 5
Function / homology
Function and homology information


protein homotrimerization / protein homodimerization activity
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #970 / Mite allergen, group 5/21 / Mite allergen, group 5/21 superfamily / Mite allergen Blo t 5 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mite allergen Blo t 5
Similarity search - Component
Biological speciesBlomia tropicalis (arthropod)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsAssigned chemical shift entry.
AuthorsNaik, M.T. / Chang, C. / Kuo, I. / Chua, K. / Huang, T.
CitationJournal: Structure / Year: 2008
Title: Roles of Structure and Structural Dynamics in the Antibody Recognition of the Allergen Proteins: An NMR Study on Blomia tropicalis Major Allergen
Authors: Naik, M.T. / Chang, C.F. / Kuo, I.C. / Kung, C.C. / Yi, F.C. / Chua, K.Y. / Huang, T.H.
History
DepositionNov 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mite allergen Blo t 5


Theoretical massNumber of molelcules
Total (without water)14,0591
Polymers14,0591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mite allergen Blo t 5 / Blo t 5 / Blo t 5


Mass: 14058.818 Da / Num. of mol.: 1 / Fragment: residues 18-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blomia tropicalis (arthropod) / Gene: BLOT5 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Keywords: Mite group 5 allergen / References: UniProt: O96870

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Assigned chemical shift entry.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNHA
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1432D 1H-1H NOESY
15215N HSQC
162TOCSY HSQC
17215N edited NOESY-HSQC
182HMBC
192HMQC
110413C Constant Time HSQC
111515N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C, U-15N] Blo t 5, 50 mM Potassium Phosphate, 100 mM Sodium Chloride, 2 mM EDTA, 0.001 % Sodium Azide, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-15N] Blo t 5, 50 mM Potassium Phosphate, 100 mM Sodium Chloride, 2 mM EDTA, 0.001 % Sodium Azide, 90% H2O, 10% D2O90% H2O/10% D2O
31 mM Blo t 5, 50 mM Potassium Phosphate, 100 mM Sodium Chloride, 2 mM EDTA, 0.001 % Sodium Azide, 100% D2O100% D2O
40.8 mM [U-10% 13C] Blo t 5, 50 mM Potassium Phosphate, 100 mM Sodium Chloride, 2 mM EDTA, 0.001 % Sodium Azide, 100% D2O100% D2O
50.8 mM [15N]-Lys,Leu Blo t 5, 50 mM Potassium Phosphate, 100 mM Sodium Chloride, 2 mM EDTA, 0.001 % Sodium Azide, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBlo t 5[U-13C; U-15N]1
50 mMPotassium Phosphate1
100 mMSodium Chloride1
2 mMEDTA1
0.001 %Sodium Azide1
1 mMBlo t 5[U-15N]2
50 mMPotassium Phosphate2
100 mMSodium Chloride2
2 mMEDTA2
0.001 %Sodium Azide2
1 mMBlo t 53
50 mMPotassium Phosphate3
100 mMSodium Chloride3
2 mMEDTA3
0.001 %Sodium Azide3
0.8 mMBlo t 5[U-10% 13C]4
50 mMPotassium Phosphate4
100 mMSodium Chloride4
2 mMEDTA4
0.001 %Sodium Azide4
0.8 mMBlo t 5[15N]-Lys,Leu5
50 mMPotassium Phosphate5
100 mMSodium Chloride5
2 mMEDTA5
0.001 %Sodium Azide5
Sample conditionspH: 7.5 / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE8003
Bruker DRXBrukerDRX6004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.112Goddardstructure solution
Sparky3.112Goddarddata analysis
XwinNMR3.5Bruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Model 21 is the average structure created in MolMol without energy minimization. Model 1 should be treated as the representative conformer.
NMR constraintsNOE constraints total: 1901 / NOE intraresidue total count: 368 / NOE long range total count: 153 / NOE medium range total count: 269 / NOE sequential total count: 316 / Hydrogen bond constraints total count: 156 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 26 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å

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