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- PDB-2mn2: 3D structure of YmoB, a modulator of biofilm formation -

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Basic information

Entry
Database: PDB / ID: 2mn2
Title3D structure of YmoB, a modulator of biofilm formation
ComponentsYmoB
KeywordsANTITOXIN / four helix bundle / buried cysteine
Function / homologyBiofilm formation regulator YbaJ / Biofilm formation regulator YbaJ / Cytoplasmic protein / Uncharacterized protein ybaJ
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodSOLUTION NMR / Simulated annealing, molecular dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsMarimon, O. / Cordeiro, T.N. / Amata, I. / Pons, M.
CitationJournal: Nat Commun / Year: 2016
Title: An oxygen-sensitive toxin-antitoxin system.
Authors: Marimon, O. / Teixeira, J.M. / Cordeiro, T.N. / Soo, V.W. / Wood, T.L. / Mayzel, M. / Amata, I. / Garcia, J. / Morera, A. / Gay, M. / Vilaseca, M. / Orekhov, V.Y. / Wood, T.K. / Pons, M.
History
DepositionMar 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: YmoB


Theoretical massNumber of molelcules
Total (without water)15,5141
Polymers15,5141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YmoB / ybaJ


Mass: 15514.276 Da / Num. of mol.: 1 / Mutation: C117S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22711 / Gene: ybaJ, YEW_DG13760, ymoB / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F4MY12, UniProt: A0A0E1NKQ3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1233D HNCO
1333D HN(CO)CA
1433D CBCA(CO)NH
1532D 1H-13C HSQC
1652D 1H-13C HSQC aliphatic Constant Time
1733D HBHA(CO)NH
1833D HN(CA)CB
1942D 1H-15N HSQC
11032D 1H-13C HSQC aliphatic
11142D 1H-13C HSQC aliphatic
11242D 1H-13C HSQC aromatic
11343D (H)CCH-TOCSY
11443D (H)CCH-TOCSY
11533D 1H-15N NOESY
11643D 1H-13C NOESY aliphatic
11743D 1H-13C NOESY aromatic
11811D 1H WATERGATE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM YmoB-C117S, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.2 mM EDTA, 0.1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] YmoB-C117S, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.2 mM EDTA, 0.1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] YmoB-C117S, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.2 mM EDTA, 0.1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] YmoB-C117S, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.2 mM EDTA, 0.1% sodium azide, 100% D2O100% D2O
51 mM [U-10% 13C; U-100% 15N] YmoB-C117S, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.2 mM EDTA, 0.1% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMYmoB-C117S-11
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMTCEP-41
0.2 mMEDTA-51
0.1 %sodium azide-61
1 mMYmoB-C117S-7[U-100% 15N]2
20 mMsodium phosphate-82
150 mMsodium chloride-92
1 mMTCEP-102
0.2 mMEDTA-112
0.1 %sodium azide-122
1 mMYmoB-C117S-13[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate-143
150 mMsodium chloride-153
1 mMTCEP-163
0.2 mMEDTA-173
0.1 %sodium azide-183
1 mMYmoB-C117S-19[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-204
150 mMsodium chloride-214
1 mMTCEP-224
0.2 mMEDTA-234
0.1 %sodium azide-244
1 mMYmoB-C117S-25[U-10% 13C; U-100% 15N]5
20 mMsodium phosphate-265
150 mMsodium chloride-275
1 mMTCEP-285
0.2 mMEDTA-295
0.1 %sodium azide-305
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Varian INOVAVarianINOVA9002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.0 and 3.0Bruker Biospincollection
VnmrJ3.2Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMRV. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburgprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
CARA1.9.0 Beta 3(c) 2000-2010 by Rochus Keller and otherschemical shift assignment
CARA1.9.0 Beta 3(c) 2000-2010 by Rochus Keller and otherspeak picking
Unio'10Version 2.0.22002-2011 Torsten Herrmannchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PyMOLSchrodinger, LLC.data analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: Simulated annealing, molecular dynamics, simulated annealing
Software ordinal: 1
NMR constraintsNOE constraints total: 1349 / NOE intraresidue total count: 541 / NOE long range total count: 214 / NOE medium range total count: 241 / NOE sequential total count: 353 / Hydrogen bond constraints total count: 72
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.2968 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.0264 Å / Maximum upper distance constraint violation: 0.0312 Å

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