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- PDB-7kwi: Solution Structure of the R2ab Repeat Domain from Staph. epidermi... -

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Basic information

Entry
Database: PDB / ID: 7kwi
TitleSolution Structure of the R2ab Repeat Domain from Staph. epidermidis Autolysin (AtlE)
ComponentsBifunctional autolysin
KeywordsHYDROLASE / SH3B fold / surface binding / extracellular
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / N-acetylmuramoyl-L-alanine amidase / amidase activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
Bifunctional autolysin
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYadav, R. / Perera, Y.R. / Fitzkee, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1818090 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI139479 United States
CitationJournal: To Be Published
Title: Solution Structure of the R2ab Repeat Domain from Staph. epidermidis Autolysin (AtlE)
Authors: Perera, Y.R. / Yadav, R. / South, T.M. / McConnell, K.D. / Fitzkee, N.C.
History
DepositionDec 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional autolysin


Theoretical massNumber of molelcules
Total (without water)16,7401
Polymers16,7401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bifunctional autolysin / AtlE


Mass: 16739.672 Da / Num. of mol.: 1 / Fragment: repeat domain (R2ab)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: atl, atlE / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: O33635, N-acetylmuramoyl-L-alanine amidase, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HN(CA)CB
132isotropic13D CBCA(CO)NH
142isotropic13D HNCA
152isotropic13D HN(CO)CA
162isotropic13D HNCO
172isotropic13D HBHA(CO)NH
182isotropic13D H(CCCO)NH
192isotropic13D (H)C(CCO)NH
1102isotropic13D 1H-15N NOESY
1113isotropic22D 1H-13C HSQC aliphatic
1123isotropic22D 1H-13C HSQC aromatic
1133isotropic23D 1H-13C NOESY aliphatic
1143isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] Autolysin repeat domain (R2ab) of Staphylococcus epidermidis, 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % w/v sodium azide, 93% H2O/7% D2O15N_R2ab93% H2O/7% D2O
solution20.5 mM [U-15N];[U-13C] Autolysin repeat domain (R2ab) of Staphylococcus epidermidis, 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % w/v sodium azide, 93% H2O/7% D2O15N13C_R2ab93% H2O/7% D2O
solution30.5 mM [U-15N];[U-13C] Autolysin repeat domain (R2ab) of Staphylococcus epidermidis, 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % w/v sodium azide, 100% D2O15N13C_R2ab100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAutolysin repeat domain (R2ab) of Staphylococcus epidermidis[U-15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.02 % w/vsodium azidenatural abundance1
0.5 mMAutolysin repeat domain (R2ab) of Staphylococcus epidermidis[U-15N];[U-13C]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.02 % w/vsodium azidenatural abundance2
0.5 mMAutolysin repeat domain (R2ab) of Staphylococcus epidermidis[U-15N];[U-13C]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.02 % w/vsodium azidenatural abundance3
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.9v1Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CARA1.9v1Keller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: cns-solve 1.3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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