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Yorodumi- PDB-2mfk: NMR solution structure of chitin-binding domain from dust mite gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mfk | ||||||
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Title | NMR solution structure of chitin-binding domain from dust mite group XII allergen Blo t 12 | ||||||
Components | Blo 1 12 | ||||||
Keywords | ALLERGEN / Chitin-binding Domain | ||||||
Function / homology | Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / chitin binding / extracellular region / Major allergen Blo t 12 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. / Kung, C.C.-H. / Huang, T. | ||||||
Citation | Journal: To be Published Title: Solution structure of Blo 1 12 CBD domain. Authors: Naik, M.T. / Kung, C.C.-H. / Huang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mfk.cif.gz | 404.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mfk.ent.gz | 340.6 KB | Display | PDB format |
PDBx/mmJSON format | 2mfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mfk_validation.pdf.gz | 520.4 KB | Display | wwPDB validaton report |
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Full document | 2mfk_full_validation.pdf.gz | 755.5 KB | Display | |
Data in XML | 2mfk_validation.xml.gz | 37 KB | Display | |
Data in CIF | 2mfk_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/2mfk ftp://data.pdbj.org/pub/pdb/validation_reports/mf/2mfk | HTTPS FTP |
-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: 7528.647 Da / Num. of mol.: 1 / Fragment: Chitin-binding domain (CBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blomia tropicalis (arthropod) / Gene: Blo t 12.0102 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q17282*PLUS |
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Sequence details | FIRST FIVE RESIDUES (GPLGS) ARE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The data deposited under this entry was used to solve structure of chitin-binding domain of allergen Blo t 12. The structure describes Blo t 12.0102 isoform identified from the mites found in Singapore. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 / 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: 1207 / NOE intraresidue total count: 264 / NOE long range total count: 468 / NOE medium range total count: 119 / NOE sequential total count: 356 / Disulfide bond constraints total count: 6 / Hydrogen bond constraints total count: 52 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 47 / Protein psi angle constraints total count: 47 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.17643 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 6.2 ° / Maximum upper distance constraint violation: 0.41 Å / Representative conformer: 1 / Torsion angle constraint violation method: PSVS | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01981 Å / Distance rms dev error: 0.01948 Å |