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Yorodumi- PDB-2mfj: Solution structure of Blo t 19, a minor dust mite allergen from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mfj | ||||||
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Title | Solution structure of Blo t 19, a minor dust mite allergen from Blomia tropicalis | ||||||
Components | Blo t 19 | ||||||
Keywords | ALLERGEN / Anti-microbial Protein | ||||||
Function / homology | Antibacterial 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 species | Blomia tropicalis (arthropod) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Naik, M.T. / Naik, N. / Huang, T. | ||||||
Citation | Journal: To be Published Title: Solution structure of Blo 1 19 Authors: Naik, M. / Naik, N. / Kuo, I. / Liao, Y. / Huang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mfj.cif.gz | 360.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mfj.ent.gz | 303.8 KB | Display | PDB format |
PDBx/mmJSON format | 2mfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/2mfj ftp://data.pdbj.org/pub/pdb/validation_reports/mf/2mfj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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Sequence details | FIRST TWO RESIDUES (GS) ARE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: 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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: NMR data was acquired at 295K using Shigemi NMR tubes. |
-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.0 / Pressure: ambient / Temperature: 295 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average 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 rms | Distance rms dev: 0.02648 Å / Distance rms dev error: 0.02581 Å |