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- PDB-2n9v: Solution NMR Structure of the membrane localization domain from P... -

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Basic information

Entry
Database: PDB / ID: 2n9v
TitleSolution NMR Structure of the membrane localization domain from Pasteurella multocida toxin
ComponentsDermonecrotic toxinCytotoxic necrotising factor family
KeywordsTOXIN / Bacterial Toxin / Membrane Localization Domains
Function / homology
Function and homology information


symbiont-mediated activation of of host transcription / symbiont-mediated killing of host cell / phospholipase activity / phospholipid binding / toxin activity / host cell plasma membrane / extracellular region / membrane / cytoplasm
Similarity search - Function
: / Pasteurella multocida toxin, C3 domain / : / Pasteurella multocida toxin, C2 domain / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesPasteurella multocida (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model8
AuthorsHisao, G.S. / Brothers, M.C. / Ho, M. / Wilson, B.A. / Rienstra, C.M.
CitationJournal: Protein Sci. / Year: 2017
Title: The membrane localization domains of two distinct bacterial toxins form a 4-helix-bundle in solution.
Authors: Hisao, G.S. / Brothers, M.C. / Ho, M. / Wilson, B.A. / Rienstra, C.M.
History
DepositionDec 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref / 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.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dermonecrotic toxin


Theoretical massNumber of molelcules
Total (without water)10,5321
Polymers10,5321
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Dermonecrotic toxin / Cytotoxic necrotising factor family / DNT / Mitogenic toxin / PMT


Mass: 10532.070 Da / Num. of mol.: 1 / Fragment: residues 589-670
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Gene: toxA / Production host: Escherichia coli (E. coli) / References: UniProt: P17452

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D (H)CCH-TOCSY
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11223D 1H-13C NOESY aromatic
11313D 1H-13C NOESY
11423D 1H-13C NOESY
11513D HNHA
11613D HN(COCA)CB
11713D HCACO
11813D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] MLDPMT, 20 mM bis-tris, 100 mM sodium chloride, 0.01 % DSS, 2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] MLDPMT, 20 mM bis-tris, 100 mM sodium chloride, 0.01 % DSS, 0.33 mM EDTA, 99% D2O99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMLDPMT-1[U-99% 13C; U-99% 15N]1
20 mMbis-tris-21
100 mMsodium chloride-31
0.01 %DSS-41
2 mMEDTA-51
1 mMMLDPMT-6[U-99% 13C; U-99% 15N]2
20 mMbis-tris-72
100 mMsodium chloride-82
0.01 %DSS-92
0.33 mMEDTA-102
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature units: K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS-NShen, Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1485 / NOE intraresidue total count: 606 / NOE long range total count: 109 / NOE medium range total count: 156 / NOE sequential total count: 238 / Protein phi angle constraints total count: 75 / Protein psi angle constraints total count: 75
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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