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- PDB-2nd9: Solution structure of MapZ extracellular domain first subdomain -

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Basic information

Entry
Database: PDB / ID: 2nd9
TitleSolution structure of MapZ extracellular domain first subdomain
ComponentsMid-cell-anchored protein Z
KeywordsCELL CYCLE / MapZ / FtsZ / peptidoglycan / division
Function / homologyMid-cell-anchored protein Z / MapZ, extracellular C-terminal domain 2 / MapZ, extracellular domain 1 / MapZ extracellular domain 1 / MapZ extracellular C-terminal domain 2 / cell cycle / cell division / plasma membrane / Mid-cell-anchored protein Z
Function and homology information
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsJean, N.L. / Manuse, S. / Guinot, M. / Bougault, C.M. / Grangeasse, C. / Simorre, J.-P.
CitationJournal: Nat Commun / Year: 2016
Title: Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ.
Authors: Manuse, S. / Jean, N.L. / Guinot, M. / Lavergne, J.P. / Laguri, C. / Bougault, C.M. / VanNieuwenhze, M.S. / Grangeasse, C. / Simorre, J.P.
History
DepositionMay 11, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_software.name / _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: Mid-cell-anchored protein Z


Theoretical massNumber of molelcules
Total (without water)14,8671
Polymers14,8671
Non-polymers00
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 / 750structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mid-cell-anchored protein Z


Mass: 14867.480 Da / Num. of mol.: 1
Fragment: First subdomain (Q178 - G313) of MapZ extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: R6 / Gene: mapZ, spr0334 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DR55

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1213D HN(CA)CO
1313D HNCO
1413D HN(CA)CB
1513D HN(COCA)CB
1613D C(CO)NH
1713D 1H-15N NOESY
1813D H(CCO)NH
1912D 1H-13C HSQC/HMQC
11012D 1H-13C HSQC/HMQC
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 2.0 mM [U-100% 13C; U-100% 15N] MapZ_extra1, 50 mM Tris, 100 mM NaCl, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMMapZ_extra1-1[U-100% 13C; U-100% 15N]1
50 mMTris-21
100 mMNaCl-31
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: 1.0 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.1W. Rieping, M. Habeck, B. Bardiaux, A. Bernard, T.E. Malliavin and M. Nilgesstructure calculation
CNS1.1A. Brunger, P. Adams, G. Clore, P. Gros, M. Nilges and R. Readrefinement
CcpNmr Analysis2.4CCPNdata analysis
TALOS+1Y. Shen, F. Delaglio, G. Cornilescu and A. Baxdata analysis
Unio10'2.0.2T. Herrmannpeak picking
NMRPipeanyF. Delaglio, S. Grzesiek,G.W. Vuister, G. Zhu, J. Pfeifer and A. Baxspectrum processing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 750 / Conformers submitted total number: 20

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