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- PDB-2mtd: Strcucture of Decorin Binding Protein A from strain PBr of Borrel... -

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Basic information

Entry
Database: PDB / ID: 2mtd
TitleStrcucture of Decorin Binding Protein A from strain PBr of Borrelia garinii
ComponentsDecorin binding protein A
KeywordsPROTEIN BINDING / adhesin / glycosaminoglycan-binding protein / lipoprotein
Function / homologyDecorin-binding protein / Decorin-binding protein / Decorin-binding superfamily / Decorin binding protein / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / Decorin binding protein A
Function and homology information
Biological speciesBorrelia garinii (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Morgan, A.
CitationJournal: Biochem.J. / Year: 2015
Title: Structural mechanisms underlying sequence-dependent variations in GAG affinities of decorin binding protein A, a Borrelia burgdorferi adhesin.
Authors: Morgan, A.M. / Wang, X.
History
DepositionAug 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 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

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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)17,9001
Polymers17,9001
Non-polymers00
Water0
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: 17899.670 Da / Num. of mol.: 1 / Fragment: UNP residues 55-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia garinii (bacteria) / Strain: PBr / Gene: BGAPBR_A0025, dbp / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8F1J8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1313D 1H-13C NOESY aliphatic
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-13C NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] PBr, 50 mM sodium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPBr-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
150 mMsodium chloride-31
Sample conditionsIonic strength: 0.2 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 140 / Protein psi angle constraints total count: 140
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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