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- PDB-6u6r: Solution NMR Structure Of The delta30-ngMinE Protein From Neisser... -

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Basic information

Entry
Database: PDB / ID: 6u6r
TitleSolution NMR Structure Of The delta30-ngMinE Protein From Neisseria gonorrheae
ComponentsCell division topological specificity factor
KeywordsCELL CYCLE / MinD / MinE / CELL DIVISION
Function / homologyCell division topological specificity factor MinE / Cell division topological specificity factor MinE superfamily / Septum formation topological specificity factor MinE / regulation of division septum assembly / cell division / identical protein binding / Cell division topological specificity factor
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodSOLID-STATE NMR / na
AuthorsCai, M. / Shen, Y. / Clore, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Probing transient excited states of the bacterial cell division regulator MinE by relaxation dispersion NMR spectroscopy.
Authors: Cai, M. / Huang, Y. / Shen, Y. / Li, M. / Mizuuchi, M. / Ghirlando, R. / Mizuuchi, K. / Clore, G.M.
History
DepositionAug 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division topological specificity factor
B: Cell division topological specificity factor


Theoretical massNumber of molelcules
Total (without water)15,2752
Polymers15,2752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1800 Å2
ΔGint-18 kcal/mol
Surface area5860 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell division topological specificity factor


Mass: 7637.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: minE / Production host: Escherichia coli (E. coli) / References: UniProt: P58152

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D CBCA(CO)NH
121isotropic23D HN(CA)CB
131isotropic23D HNCO
141isotropic23D HBHA(CBCACO)NH
153isotropic23D CBCA(CO)NH
163isotropic23D HBHA(CBCACO)NH
173isotropic23D HNCO
183isotropic23D HN(CA)CB
292anisotropic3HSQC IPAP
2102isotropic3HSQC IPAP
2114anisotropic3HSQC IPAP
2124isotropic3HSQC IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM U-13C/15N MinE-d30, 95% H2O/5% D2OU-13C/15N_sample_d3095% H2O/5% D2O
solution21 mM U-2H/15N MinE-d30-RDC, 1 mM U-2H/15N MinE-d30-CPMG, 90% H2O/10% D2OU-2H/15N_sample_d3090% H2O/10% D2O
solution31 mM U-13C/15N MinE-d30-I24N, 95% H2O/5% D2OU-13C/15N_sample_d30_I24N95% H2O/5% D2O
solution41 mM 2H/15N MinE-d30-I24N-RDC, 1 mM 2H/15N MinE-d30-I24N-CPMG, 90% H2O/10% D2OU-2H/15N_sample_d30_I24N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMinE-d30U-13C/15N1
1 mMMinE-d30-RDCU-2H/15N2
1 mMMinE-d30-CPMGU-2H/15N2
1 mMMinE-d30-I24NU-13C/15N3
1 mMMinE-d30-I24N-RDC2H/15N4
1 mMMinE-d30-I24N-CPMG2H/15N4
25 mMpotassium phosphatenatural abundance1
25 mMpotassium phosphatenatural abundance3
0.5 mMEDTAnatural abundance1
0.5 mMEDTAnatural abundance3
0.1 mMbenzamidine chloridenatural abundance1
0.1 mMbenzamidine chloridenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
125 mMMinE-CN6.51 bar298 K
2200 mMMinE-RDC6.51 bar298 K+ 200 mM NaCl,11mg/ml phage pf1 and 10% (v/v) D2O instead 5% (v/v) D2O

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
PIPPGarrettchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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