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- PDB-2mpk: Characterization and structure of the MIT1 domain of a chitin syn... -

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Basic information

Entry
Database: PDB / ID: 2mpk
TitleCharacterization and structure of the MIT1 domain of a chitin synthase from the Oomycete Saprolegnia monoica
ComponentsChitin synthase 1
KeywordsTRANSFERASE / MIT domain / three-helix bundle / Saprolegnia / Oomycete / carbohydrate synthase / microtubule interacting and trafficking domain
Function / homology
Function and homology information


chitin biosynthetic process / chitin synthase / chitin synthase activity / membrane => GO:0016020
Similarity search - Function
Chitin synthase N-terminal / Chitin synthase N-terminal / Fungal chitin synthase / Chitin synthase / Chitin synthase / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / Nucleotide-diphospho-sugar transferases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaprolegnia monoica (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBulone, V. / Szpryngiel, S. / Brown, C. / Ye, W.
CitationJournal: Febs J. / Year: 2016
Title: Structural and functional characterization of the microtubule interacting and trafficking domains of two oomycete chitin synthases.
Authors: Brown, C. / Szpryngiel, S. / Kuang, G. / Srivastava, V. / Ye, W. / McKee, L.S. / Tu, Y. / Maler, L. / Bulone, V.
History
DepositionMay 27, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 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 / 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_database_status.status_code_nmr_data / _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: Chitin synthase 1


Theoretical massNumber of molelcules
Total (without water)8,5281
Polymers8,5281
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Chitin synthase 1 /


Mass: 8527.657 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 103-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saprolegnia monoica (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D7NQS8, chitin synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.3-1.0 mM [U-100% 13C; U-100% 15N] SmChs_MIT1-1, 10 % D2O-2, 50 mM sodium phosphate-3, 150 mM sodium chloride-4, 90 % H2O-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSmChs_MIT1-1[U-100% 13C; U-100% 15N]0.3-1.01
10 %D2O-21
50 mMsodium phosphate-31
150 mMsodium chloride-41
90 %H2O-51
Sample conditionsIonic strength: 200 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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