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- PDB-1j3g: Solution structure of Citrobacter Freundii AmpD -

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Basic information

Entry
Database: PDB / ID: 1j3g
TitleSolution structure of Citrobacter Freundii AmpD
ComponentsAmpD proteinPyotraumatic dermatitis
KeywordsHYDROLASE / MIXED ALPHA-BETA
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / metal ion binding / cytoplasm
Similarity search - Function
Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiepinsh, E. / Genereux, C. / Dehareng, D. / Joris, B. / Otting, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: NMR Structure of Citrobacter freundii AmpD, Comparison with Bacteriophage T7 Lysozyme and Homology with PGRP Domains
Authors: Liepinsh, E. / Genereux, C. / Dehareng, D. / Joris, B. / Otting, G.
History
DepositionJan 31, 2003Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 18, 2003ID: 1IYA, 1J2S
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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: AmpD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9372
Polymers20,8711
Non-polymers651
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein AmpD protein / Pyotraumatic dermatitis / AmpD


Mass: 20871.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Plasmid: pET-9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D-NOESY
1223D 15N-separated NOESY
132HNHB
143DQF-COSY
152CT-HMQC-HN
NMR detailsText: The structure was determined by triple-resonance and 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3mM AmpD U-15N,13C95% H2O, 5% D2O, 2mM ZnSO4
20.3mM AmpD U-15N95% H2O, 5% D2O, 2mM ZnSO4
30.3mM AmpD95% H2O, 5% D2O, 2mM ZnSO4
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
PROSA3.6Guentertprocessing
XEASY970326Bartelsdata analysis
DYANA1.5Guentertstructure solution
OPAL2.6P.Luginbuhl,P.Guntert,M.Billeter,K.Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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