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- PDB-6mk7: Solution structure of the large extracellular loop of FtsX in Str... -

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Basic information

Entry
Database: PDB / ID: 6mk7
TitleSolution structure of the large extracellular loop of FtsX in Streptococcus pneumoniae
ComponentsCell division protein FtsX
KeywordsMEMBRANE PROTEIN / CELL WALL / PEPTIDOGLYCAN / CELL DIVISION
Function / homologyCell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC3 transporter permease protein domain / FtsX-like permease family / cell cycle / cell division / plasma membrane / Cell division protein FtsX
Function and homology information
Biological speciesStreptococcus pneumoniae serotype 2
MethodSOLUTION NMR / simulated annealing
AuthorsEdmonds, K.A. / Fu, Y. / Wu, H. / Rued, B.E. / Bruce, K.E. / Winkler, M.E. / Giedroc, D.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM109825 United States
CitationJournal: MBio / Year: 2019
Title: Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae.
Authors: Rued, B.E. / Alcorlo, M. / Edmonds, K.A. / Martinez-Caballero, S. / Straume, D. / Fu, Y. / Bruce, K.E. / Wu, H. / Havarstein, L.S. / Hermoso, J.A. / Winkler, M.E. / Giedroc, D.P.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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: Cell division protein FtsX


Theoretical massNumber of molelcules
Total (without water)14,0131
Polymers14,0131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The relative quality of TROSY and HSQC spectra show that this domain is a monomer by NMR
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cell division protein FtsX /


Mass: 14013.403 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: ftsX, SPD_0660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04LE4

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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
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D C(CO)NH
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
191isotropic13D HNCO
1101isotropic13D H(CCO)NH
1112isotropic13D (H)CCH-TOCSY
1122isotropic13D (H)CCH-COSY
1131isotropic13D 1H-15N NOESY
1142isotropic13D 1H-13C NOESY aliphatic
1152isotropic13D 1H-13C NOESY aromatic
1161isotropic22D IPAP 1H-15N HSQC
1173anisotropic22D IPAP 1H-15N HSQC
1182isotropic12D HBCBCGCDHE
1192isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-99% 13C; U-99% 15N] FtsX extracellular loop 1, 90 % H2O, 10 % [U-99% 2H] D2O, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2 mM DSS, 90% H2O/10% D2OH2O_sample90% H2O/10% D2O
solution30.4 mM [U-99% 13C; U-99% 15N] FtsX extracellular loop 1, 90 % H2O, 10 % [U-99% 2H] D2O, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2 mM DSS, 20 mg/mL Pf1 phage, 90% H2O/10% D2Ophage90% H2O/10% D2O
solution20.7 mM [U-99% 13C; U-99% 15N] FtsX extracellular loop 1, 100 % [U-99% 2H] D2O, 50 mM potassium phosphate, 50 mM sodium chloride, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMFtsX extracellular loop 1[U-99% 13C; U-99% 15N]1
90 %H2Onatural abundance1
10 %D2O[U-99% 2H]1
50 mMpotassium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.2 mMDSSnatural abundance1
0.4 mMFtsX extracellular loop 1[U-99% 13C; U-99% 15N]3
90 %H2Onatural abundance3
10 %D2O[U-99% 2H]3
50 mMpotassium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.2 mMDSSnatural abundance3
20 mg/mLPf1 phagenatural abundance3
0.7 mMFtsX extracellular loop 1[U-99% 13C; U-99% 15N]2
100 %D2O[U-99% 2H]2
50 mMpotassium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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