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- PDB-2mfj: Solution structure of Blo t 19, a minor dust mite allergen from B... -

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Basic information

Entry
Database: PDB / ID: 2mfj
TitleSolution structure of Blo t 19, a minor dust mite allergen from Blomia tropicalis
ComponentsBlo t 19
KeywordsALLERGEN / Anti-microbial Protein
Function / homologyAntibacterial factor-related peptide / Antibacterial factor-related peptide superfamily / Nematode antimicrobial peptide / defense response to other organism / Blo t 19 allergen
Function and homology information
Biological speciesBlomia tropicalis (arthropod)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsNaik, M.T. / Naik, N. / Huang, T.
CitationJournal: To be Published
Title: Solution structure of Blo 1 19
Authors: Naik, M. / Naik, N. / Kuo, I. / Liao, Y. / Huang, T.
History
DepositionOct 15, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blo t 19


Theoretical massNumber of molelcules
Total (without water)6,9461
Polymers6,9461
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)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Blo t 19


Mass: 6945.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blomia tropicalis (arthropod) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W5RZ24*PLUS
Has protein modificationY
Sequence detailsFIRST TWO RESIDUES (GS) ARE EXPRESSION TAGS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The data from this entry were used to determine structure of Blo t 19. Due to Proline isomerization, Blo t 19 spectrum has degenerate resonances for a stretch of six residues in its C- ...Details: The data from this entry were used to determine structure of Blo t 19. Due to Proline isomerization, Blo t 19 spectrum has degenerate resonances for a stretch of six residues in its C-terminus. These two populations have varying intensities and are unambiguously assigned as major and minor population. Solution structure is calculated for the Major population.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNHA
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11112D-(HB)CB(CGCD)HD
11212D-(HB)CB(CGCDCE)HE
11332D-TOCSY
11423D 1H-15N TOCSY
11532D 1H-1H NOESY
11613D 1H-13C NOESYHSQC
11713D 1H-15N NOESYHSQC
11842D 1H-15N IPAP HSQC
NMR detailsText: NMR data was acquired at 295K using Shigemi NMR tubes.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Blo t 19-1, 50 mM potassium phosphate-2, 100 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] Blo t 19-4, 50 mM potassium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
31 mM Blo t 19-7, 50 mM potassium phosphate-8, 100 mM sodium chloride-9, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 15N] Blo t 19-10, 50 mM potassium phosphate-11, 100 mM sodium chloride-12, 15 mg/ml Pf1 phage-13, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBlo t 19-1[U-100% 13C; U-100% 15N]1
50 mMpotassium phosphate-21
100 mMsodium chloride-31
1 mMBlo t 19-4[U-100% 15N]2
50 mMpotassium phosphate-52
100 mMsodium chloride-62
1 mMBlo t 19-73
50 mMpotassium phosphate-83
100 mMsodium chloride-93
1 mMBlo t 19-10[U-100% 15N]4
50 mMpotassium phosphate-114
100 mMsodium chloride-124
15 mg/mLPf1 phage-134
Sample conditionspH: 6 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE8504

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3.9Guntert, Mumenthaler and Wuthrichgeometry optimization
PSVS1.5Bhattacharya and Montelionevalidation
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
Details: Initial structure ensemble was calculated by semi-automated NOESY assignment by CYANA. The assignments were manually verified in Sparky and final structure annealing was performed in CYANA. ...Details: Initial structure ensemble was calculated by semi-automated NOESY assignment by CYANA. The assignments were manually verified in Sparky and final structure annealing was performed in CYANA. Structure and restraints from CYANA were imported in Xplor-NIH for explicit water refinement.
NMR constraintsNOE constraints total: 1140 / NOE intraresidue total count: 212 / NOE long range total count: 294 / NOE medium range total count: 314 / NOE sequential total count: 320 / Disulfide bond constraints total count: 12 / Hydrogen bond constraints total count: 54 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 43 / Protein phi angle constraints total count: 39 / Protein psi angle constraints total count: 39
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.08688 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.9 ° / Maximum upper distance constraint violation: 0.7 Å / Representative conformer: 1 / Torsion angle constraint violation method: PSVS
NMR ensemble rmsDistance rms dev: 0.02648 Å / Distance rms dev error: 0.02581 Å

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