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- PDB-2kt7: Solution NMR structure of mucin-binding domain of protein lmo0835... -

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Basic information

Entry
Database: PDB / ID: 2kt7
TitleSolution NMR structure of mucin-binding domain of protein lmo0835 from Listeria monocytogenes, Northeast Structural Genomics Consortium Target LmR64A
ComponentsPutative peptidoglycan bound protein (LPXTG motif)
KeywordsCELL ADHESION / MEMBRANE PROTEIN / immunoglobulin fold / all-beta / peptidoglycan binding protein / LPXTG motif / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
Putative peptidoglycan bound protein (lpxtg motif) / MucBP domain / MucBP domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Putative peptidoglycan bound protein (LPXTG motif)
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / He, Y. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of mucin-binding domain of protein lmo0835 from Listeria monocytogenes
Authors: Eletsky, A. / He, Y. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJan 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptidoglycan bound protein (LPXTG motif)


Theoretical massNumber of molelcules
Total (without water)11,5021
Polymers11,5021
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative peptidoglycan bound protein (LPXTG motif)


Mass: 11501.717 Da / Num. of mol.: 1 / Fragment: sequence database residues 34-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0835 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8Y8R0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 15N T1
1211D 15N T2
1312D 1H-15N HSQC
1412D 1H-13C CT-HSQC aliphatic
1512D 1H-13C CT-HSQC aromatic
1613D HNCO
1713D CBCA(CO)NH
1813D HN(CA)CO
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY aliphatic
11213D (H)CCH-COSY aliphatic
11313D (H)CCH-COSY aromatic
11413D 1H-15N,13C NOESY
11522D 1H-15N LR-HSQC (Histidine)
11622D 1H-13C CT-HSQC methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-13C; U-15N] lmr64a protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.9 mM [U-5% 13C; U-15N] lmr64ab protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMlmr64a_protein-1[U-13C; U-15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.01 %sodium azide-51
0.9 mMlmr64a_protein-6[U-5% 13C; U-15N]2
20 mMMES-72
100 mMsodium chloride-82
5 mMcalcium chloride-92
0.01 %sodium azide-102
Sample conditionsIonic strength: 225 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.4Guntertprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxdata analysis
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.4Bhattacharya and Montelionevalidation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The programs CYANA and AutoStructure were used to derive consensus peak assignments followed by iterative refinement with CYANA using NOE-based constraints and PHI and PSI dihedral angle ...Details: The programs CYANA and AutoStructure were used to derive consensus peak assignments followed by iterative refinement with CYANA using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 2129 / NOE intraresidue total count: 370 / NOE long range total count: 841 / NOE medium range total count: 284 / NOE sequential total count: 634 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 52 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.1 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.75 ° / Maximum upper distance constraint violation: 1.97 Å
NMR ensemble rmsDistance rms dev: 0.02 Å

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