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- PDB-2lqu: Structure of decorbin-binding protein A from Borrelia burgdorferi -

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Basic information

Entry
Database: PDB / ID: 2lqu
TitleStructure of decorbin-binding protein A from Borrelia burgdorferi
ComponentsDecorin-binding protein A
KeywordsCELL ADHESION / GAG-binding protein / helical bundle protein / Lyme disease / bacterial adhesin
Function / homology
Function and homology information


Decorin-binding protein / : / Decorin-binding protein / Decorin-binding superfamily / Decorin binding protein / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Decorin-binding protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsWang, X.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of decorin-binding protein A from Borrelia burgdorferi.
Authors: Wang, X.
History
DepositionMar 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: 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 / 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 / _struct_ref_seq_dif.details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decorin-binding protein A


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
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)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Decorin-binding protein A


Mass: 18555.178 Da / Num. of mol.: 1 / Fragment: UNP residues 26-191 / Mutation: C25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: BB_A24, dbpA / Production host: Escherichia coli (E. coli) / Strain (production host): B21 / Variant (production host): DE3 / References: UniProt: O50917
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1613D (H)CCH-TOCSY
172J-MODULATED 15N HSQC
182JNC-MODULATED 15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] DBPA, 50 mM sodium phosphate, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] DBPA, 50 mM sodium phosphate, 10 % D2O, 5 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDBPA-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
10 %D2O-31
0.8 mMDBPA-4[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate-52
10 %D2O-62
5 %polyacrylamide-72
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Inova 800 / Manufacturer: Agilent / Model: Inova 800 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: XPLOR-NIH refinement with RDCs
NMR constraintsNOE constraints total: 1288 / NOE intraresidue total count: 198 / NOE long range total count: 452 / NOE medium range total count: 396 / NOE sequential total count: 242 / Protein phi angle constraints total count: 105 / Protein psi angle constraints total count: 105
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 0.3 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 10 ° / Maximum upper distance constraint violation: 0.49 Å
NMR ensemble rmsDistance rms dev: 0.05 Å

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