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- PDB-2kac: NMR solution structure of KX6E protL mutant -

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Basic information

Entry
Database: PDB / ID: 2kac
TitleNMR solution structure of KX6E 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
Model detailsHALOPHILIC MUTANT OF PROTL
AuthorsLopez-Mendez, B. / Tadeo, X. / Pons, M. / Millet, O.
Citation
Journal: Plos Biol. / Year: 2009
Title: Structural basis for the aminoacid composition of proteins from halophilic archea
Authors: Tadeo, X. / Lopez-Mendez, B. / Trigueros, T. / Lain, A. / Castano, D. / Millet, O.
#1: Journal: 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
DepositionNov 4, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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)7,0211
Polymers7,0211
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 #1lowest energy

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Components

#1: Protein Protein L /


Mass: 7021.356 Da / Num. of mol.: 1 / Fragment: residues in database 111-173 / Mutation: K23E,K28E,K41E,K42E,K54E,K61E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptostreptococcus magnus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51912

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] Kx6E PROTL MUTANT, 500mM sodium chloride, 20mM sodium phosphate, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKx6E PROTL MUTANT[U-99% 13C; U-99% 15N]1
500 mMsodium chloride1
20 mMsodium phosphate1
Sample conditionsIonic strength: 500 / pH: 6 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.6P.Guntert, et al.structure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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