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- PDB-2mm8: Structural and biochemical characterization of Jaburetox -

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Basic information

Entry
Database: PDB / ID: 2mm8
TitleStructural and biochemical characterization of Jaburetox
ComponentsUrease
KeywordsHYDROLASE / disordered protein
Function / homology
Function and homology information


urease / urease activity / urea catabolic process / nickel cation binding
Similarity search - Function
Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit ...Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsDobrovolska, O. / Lopez, F. / Ciurli, S. / Zambelli, B. / Carlini, C.
CitationJournal: To be Published
Title: 1H, 13C, 15N resonance assignments of reduced Jaburetox
Authors: Dobrovolska, O. / Lopez, F. / Zambelli, B. / Carlini, C. / Ciurli, S.
History
DepositionMar 12, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2May 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: Urease


Theoretical massNumber of molelcules
Total (without water)10,9691
Polymers10,9691
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)5 / 5all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein Urease / Urea amidohydrolase


Mass: 10969.163 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 230-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Gene: JBURE-II / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E6Y5X0, urease

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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(CO)CA
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D 1H-15N TOCSY
11013D (H)CCH-TOCSY
11113D HBHA(CO)NH

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] Jbtx-1, 50 mM sodium phosphate-2, 1 mM EDTA-3, 1 mM TCEP-4, 5 % D2O-5, 95 % H2O-6, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMJbtx-1[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate-21
1 mMEDTA-31
1 mMTCEP-41
5 %D2O-51
95 %H2O-61
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5 / Representative conformer: 1

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