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- PDB-2mey: RDC refined solution structure of Blo t 5. -

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Basic information

Entry
Database: PDB / ID: 2mey
TitleRDC refined solution structure of Blo t 5.
ComponentsMite allergen Blo t 5
KeywordsALLERGEN
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 / simulated annealing
Model detailslowest energy, model1
AuthorsNaik, M.T. / Huang, T.
Citation
Journal: To be Published
Title: NMR structure note: Blo t 5 from Blomia Tropicalis
Authors: Naik, M.T. / Naik, N. / Huang, T.
#1: Journal: J.Biomol.Nmr / Year: 2007
Title: Complete 1H, 13C and 15N resonance assignments of Blo t 5, a major mite allergen from Blomia tropicalis.
Authors: Naik, M.T. / Chang, C.F. / Kuo, I.C. / Yu, T. / Fang, P.J. / Chua, K.Y. / Huang, T.H.
History
DepositionOct 2, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 5, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)20 / 400structures 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: UNP RESIDUES 18-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blomia tropicalis (arthropod) / Gene: BLOT5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O96870

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This structure uses all restraints used to calculate entry 2JMH. In addition extensive new RDC data was used and final structure ensemble underwent explicit water refinement. Still 2JMH is ...Details: This structure uses all restraints used to calculate entry 2JMH. In addition extensive new RDC data was used and final structure ensemble underwent explicit water refinement. Still 2JMH is now an old and widely cited structure and may *not be replaced. The main purpose of this new entry is to validate the accuracy of 2JMH. (Mueller et al. JBC (2010) 285, 25394).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
114IPAP-15N-HSQC
124IPAP-J-HNCO
133IPAP-15N-HSQC
141IPAP-15N-HSQC
151IPAP-15N HSQC
161IPAP-J-HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] Blo t 5-1, 50 mM Potassium Phosphate-2, 100 mM Sodium Chloride-3, 2 mM EDTA-4, 0.001 % Sodium Azide-5, 14 mg/mL Pf1 phage-6, 1 mM [U-13C; U-15N] Blo t 5-7, 50 mM Potassium Phosphate-8, 100 mM Sodium Chloride-9, 2 mM EDTA-10, 0.001 % Sodium Azide-11, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N] Blo t 5-12, 50 mM Potassium Phosphate-13, 100 mM Sodium Chloride-14, 2 mM EDTA-15, 0.001 % Sodium Azide-16, 4 % C12E5/n-hexanol-17, 1 mM [U-15N] Blo t 5-18, 50 mM Potassium Phosphate-19, 100 mM Sodium Chloride-20, 2 mM EDTA-21, 0.001 % Sodium Azide-22, 6 % Polyacrylamide Gel-23, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-15N] Blo t 5-24, 50 mM Potassium Phosphate-25, 100 mM Sodium Chloride-26, 2 mM EDTA-27, 0.001 % Sodium Azide-28, 4 % C12E5/n-hexanol-29, 1 mM [U-15N] Blo t 5-30, 50 mM Potassium Phosphate-31, 100 mM Sodium Chloride-32, 2 mM EDTA-33, 0.001 % Sodium Azide-34, 6 % Polyacrylamide Gel-35, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-13C; U-15N] Blo t 5-36, 50 mM Potassium Phosphate-37, 100 mM Sodium Chloride-38, 2 mM EDTA-39, 0.001 % Sodium Azide-40, 14 mg/mL Pf1 phage-41, 1 mM [U-13C; U-15N] Blo t 5-42, 50 mM Potassium Phosphate-43, 100 mM Sodium Chloride-44, 2 mM EDTA-45, 0.001 % Sodium Azide-46, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBlo t 5-1[U-13C; U-15N]1
50 mMPotassium Phosphate-21
100 mMSodium Chloride-31
2 mMEDTA-41
0.001 %Sodium Azide-51
14 mg/mLPf1 phage-61
1 mMBlo t 5-7[U-13C; U-15N]1
50 mMPotassium Phosphate-81
100 mMSodium Chloride-91
2 mMEDTA-101
0.001 %Sodium Azide-111
1 mMBlo t 5-12[U-15N]2
50 mMPotassium Phosphate-132
100 mMSodium Chloride-142
2 mMEDTA-152
0.001 %Sodium Azide-162
4 %C12E5/n-hexanol-172
1 mMBlo t 5-18[U-15N]2
50 mMPotassium Phosphate-192
100 mMSodium Chloride-202
2 mMEDTA-212
0.001 %Sodium Azide-222
6 %Polyacrylamide Gel-232
1 mMBlo t 5-24[U-15N]3
50 mMPotassium Phosphate-253
100 mMSodium Chloride-263
2 mMEDTA-273
0.001 %Sodium Azide-283
4 %C12E5/n-hexanol-293
1 mMBlo t 5-30[U-15N]3
50 mMPotassium Phosphate-313
100 mMSodium Chloride-323
2 mMEDTA-333
0.001 %Sodium Azide-343
6 %Polyacrylamide Gel-353
1 mMBlo t 5-36[U-13C; U-15N]4
50 mMPotassium Phosphate-374
100 mMSodium Chloride-384
2 mMEDTA-394
0.001 %Sodium Azide-404
14 mg/mLPf1 phage-414
1 mMBlo t 5-42[U-13C; U-15N]4
50 mMPotassium Phosphate-434
100 mMSodium Chloride-444
2 mMEDTA-454
0.001 %Sodium Azide-464
Sample conditionspH: 7.5 / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Brukernmr data acquisition
TopSpin3Brukerprocessing
Sparky3.112UCSFnmr data analysis
Sparky3.112UCSFstructure solution
Sparky3.112Guntert, Mumenthaler and Wuthrichnmr data analysis
Sparky3.112Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.112UCSFnmr data analysis
Sparky3.112UCSFstructure solution
Sparky3.112Guntert, Mumenthaler and Wuthrichnmr data analysis
Sparky3.112Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
PALESM. Zweckstetter and A. Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Explicit water refinement
NMR constraintsNOE constraints total: 1105 / NOE intraresidue total count: 368 / NOE long range total count: 153 / NOE medium range total count: 269 / NOE sequential total count: 315 / Hydrogen bond constraints total count: 156 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / 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: 0.06289 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 12.61 ° / Maximum upper distance constraint violation: 0.69 Å / Representative conformer: 1 / Torsion angle constraint violation method: PSVS
NMR ensemble rmsDistance rms dev: 0.034 Å / Distance rms dev error: 0.004 Å

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