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- PDB-9oiu: Soltion Structure of His6-Small Ubiquitin-like Modifier (His6-SUMO) -

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Basic information

Entry
Database: PDB / ID: 9oiu
TitleSoltion Structure of His6-Small Ubiquitin-like Modifier (His6-SUMO)
ComponentsHexa Histidine Small Ubiquitin-like Modifier (His6-SUMO)
KeywordsBIOSYNTHETIC PROTEIN / Expression System / Protein purification / SPI 2.0 / pSPIH6 / Fusion protein
Biological speciesLactococcus garvieae (lactic acid bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsMallett, T.M. / Lamer, T.D. / Vederas, J.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Not funded Canada
CitationJournal: Int J Mol Sci / Year: 2025
Title: Solution Structure of the Broad-Spectrum Bacteriocin Garvicin Q.
Authors: Mallett, T. / Lamer, T. / Aleksandrzak-Piekarczyk, T. / McKay, R.T. / Catenza, K. / Sit, C. / Rainey, J.K. / Towle-Straub, K.M. / Vederas, J.C. / van Belkum, M.J.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexa Histidine Small Ubiquitin-like Modifier (His6-SUMO)


Theoretical massNumber of molelcules
Total (without water)13,4401
Polymers13,4401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hexa Histidine Small Ubiquitin-like Modifier (His6-SUMO)


Mass: 13440.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae (lactic acid bacteria)
Strain: BCC 43578 / Plasmid: pSPIH6 / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic13D HNCA
131anisotropic13D HN(CO)CA
141anisotropic13D CBCA(CO)NH
151anisotropic13D HNHA
161anisotropic13D HN(CA)CB
171anisotropic13D HNCO
181anisotropic13D HN(CA)CO
191anisotropic13D 1H-15N TOCSY
1101anisotropic13D 1H-15N NOESY
1111anisotropic23D (H)CCH-TOCSY
1121anisotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] Hexa Histidine Small Ubiquitin-like Modifier (His6-SUMO), 10 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O
Label: 13C,15N_His6-SUMO / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHexa Histidine Small Ubiquitin-like Modifier (His6-SUMO)[U-99% 13C; U-99% 15N]1
10 mMsodium phosphatenatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Ionic strength err: 0.01 / Label: SUMO_conditions / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 300.5 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA6001University of Alberta, department of chemistry. Agilent/Varian VNMRS four-channel 600 MHz spectrometer with an autoxid HCN probe
Bruker AVIIIHDBrukerAVIIIHD8002QANUC 800, McGill University, Chemistry characterization facility

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis3.2.12CCPNchemical shift assignment
X-PLOR NIH3.9.8Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOS-N4.01Adriaan Baxgeometry optimization
PdbStatwwPDB Validation Report Servicerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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