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- PDB-2jzp: NMR solution structure of Kx5Q ProtL mutant -

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Basic information

Entry
Database: PDB / ID: 2jzp
TitleNMR solution structure of Kx5Q ProtL mutant
ComponentsProtein L
KeywordsIMMUNE SYSTEM / protein / Cell wall / Peptidoglycan-anchor
Function / homology
Function and homology information


molecular adaptor activity / metal ion binding
Similarity search - Function
Protein L, Ig light chain-binding / Repeat of unknown function DUF5633 / Protein L b1 domain / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesPeptostreptococcus magnus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLopez-Mendez, N. / Tadeo, X. / Castano, D. / Pons, M. / Millet Aguilar-Galindo, O.
CitationJournal: Biophys.J. / Year: 2009
Title: Protein stabilization and the hofmeister effect: the role of hydrophobic solvation
Authors: Tadeo, X. / Lopez-Mendez, B. / Castano, D. / Trigueros, T. / Millet, O.
History
DepositionJan 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein L


Theoretical massNumber of molelcules
Total (without water)7,0161
Polymers7,0161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein L /


Mass: 7016.498 Da / Num. of mol.: 1 / Fragment: sequence database residues 111-173 / Mutation: K23Q, K28Q, K42Q, K54Q, K61Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptostreptococcus magnus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE(3) / References: UniProt: Q51912

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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-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNHA
1913D (H)CCH-COSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] ProtL5Q, 20 mM sodium phosphate, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMProtL5Q[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate1
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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