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- PDB-2n45: EC-NMR Structure of Escherichia coli Maltose-binding protein Dete... -

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Basic information

Entry
Database: PDB / ID: 2n45
TitleEC-NMR Structure of Escherichia coli Maltose-binding protein Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data with a second set of RDC data simulated for an alternative alignment tensor. Northeast Structural Genomics Consortium target ER690
ComponentsMaltose-binding periplasmic protein
KeywordsPERIPLASMIC BINDING PROTEIN / EC-NMR / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / PROTEIN STRUCTURE INITIATIVE
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 0THIS ENTRY 2N45 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN PDB ENTRIES ...THIS ENTRY 2N45 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN PDB ENTRIES 2MV0 AND 1EZP DETERMINED BY AUTHORS: P.ROSSI,O.F.LANGE,N.G.SGOURAKIS,Y.SONG,H.LEE,J.M.ARAMINI,A.ERTEKIN,R.XIAO,T.B.ACTON,D.BAKER,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) (PDB ENTRY 2MV0); G.A.MUELLER,W.Y.CHOY,D.YANG,J.D.FORMAN-KAY,R.A.VENTERS,L.E.KAY (PDB ENTRY 1EZP).

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)40,7531
Polymers40,7531
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 40753.152 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE, b4034, JW3994 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHORS USED THE CS DATA AND THE NOESY PEAK LIST DATA FROM PDB ENTRY 2MV0, AND THE RDC DATA FROM PDB ENTRY 1EZP.

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Sample preparation

SampleConc.: 1.05 mM / Component: MBP-1

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Processing

NMR software
NameDeveloperClassification
EVfold-plmdata analysis
ASDP (EC-NMR)data analysis
CYANAdata analysis
RosettaBaker, D. et al.refinement
TALOS+data analysis
ReduceRichardson, J. & Richardson, D.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: PROTONS FROM THE ROSETTA MODELS WERE REMOVED AND ADDED BACK USING REDUCE. REDCAT WAS USED TO SIMULATE ONE RDC DATA SET WITH ONE ALIGNMENT TENSOR FROM THE REFERENCE STRUCTURE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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