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- PDB-2mfk: NMR solution structure of chitin-binding domain from dust mite gr... -

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Basic information

Entry
Database: PDB / ID: 2mfk
TitleNMR solution structure of chitin-binding domain from dust mite group XII allergen Blo t 12
ComponentsBlo 1 12
KeywordsALLERGEN / Chitin-binding Domain
Function / homologyChitin 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 speciesBlomia tropicalis (arthropod)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsNaik, M.T. / Kung, C.C.-H. / Huang, T.
CitationJournal: To be Published
Title: Solution structure of Blo 1 12 CBD domain.
Authors: Naik, M.T. / Kung, C.C.-H. / 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 1.2Oct 30, 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 1 12


Theoretical massNumber of molelcules
Total (without water)7,5291
Polymers7,5291
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 1 12


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
Has protein modificationY
Sequence detailsFIRST FIVE RESIDUES (GPLGS) ARE EXPRESSION TAGS

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Experimental details

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Experiment

ExperimentMethod: 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.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D H(CCO)NH
1813D CC(CO)NH
1913D (H)CCH-COSY
11013D HBHA(CO)NH
11112D-(HB)CB(CGCD)HD
11213D 1H-13C NOESYHSQC
11313D 1H-15N NOESYHSQC
11432D 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 12 CBD-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 12 CBD-4, 50 mM potassium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] Blo t 12 CBD-7, 50 mM potassium phosphate-8, 100 mM sodium chloride-9, 11 mg/ml Pf1 phage-10, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBlo t 12 CBD-1[U-100% 13C; U-100% 15N]1
50 mMpotassium phosphate-21
100 mMsodium chloride-31
1 mMBlo t 12 CBD-4[U-100% 15N]2
50 mMpotassium phosphate-52
100 mMsodium chloride-62
1 mMBlo t 12 CBD-7[U-100% 15N]3
50 mMpotassium phosphate-83
100 mMsodium chloride-93
11 mg/mLPf1 phage-103
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

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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: 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 representativeSelection criteria: lowest energy
NMR ensembleAverage 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 rmsDistance rms dev: 0.01981 Å / Distance rms dev error: 0.01948 Å

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