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- PDB-7pmp: Solution structure of Legionella pneumophila LspD -

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Basic information

Entry
Database: PDB / ID: 7pmp
TitleSolution structure of Legionella pneumophila LspD
ComponentsType II protein secretion LspD
KeywordsPROTEIN TRANSPORT / Legionella pneumophila / Type II Secretion System / GspD / Recognition
Function / homology
Function and homology information


peptidoglycan binding / protein secretion / cell outer membrane
Similarity search - Function
Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / GspD/PilQ family / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Type II protein secretion LspD
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPortlock, T.J. / Garnett, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council1806169 United Kingdom
CitationJournal: To Be Published
Title: Solution structure of Legionella pneumophila LspD N0
Authors: Portlock, T.J. / Garnett, J.A.
History
DepositionSep 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II protein secretion LspD


Theoretical massNumber of molelcules
Total (without water)12,2951
Polymers12,2951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Type II protein secretion LspD


Mass: 12295.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lspD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7I3K3

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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
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D (H)CCH-TOCSY
151isotropic13D CCH-TOCSY
161isotropic13D HNCA
1101isotropic13D HN(CO)CA
191isotropic13D HN(CA)CB
181isotropic13D 1H-13C NOESY
171isotropic13D 1H-15N NOESY
1111isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-99% 13C; U-99% 15N] LspD N0, 50 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMLspD N0[U-99% 13C; U-99% 15N]1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 50 mM NaCl, 50 mM sodium phosphate Not defined
Label: Condition1 / pH: 7.0 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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