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- PDB-2k1f: SUMO-3 from Drosophila melanogaster (dsmt3) -

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Basic information

Entry
Database: PDB / ID: 2k1f
TitleSUMO-3 from Drosophila melanogaster (dsmt3)
ComponentsCG4494-PA
KeywordsUNKNOWN FUNCTION / dSUMO / dsmt3 / drosophila SUMO
Function / homology
Function and homology information


Vitamin D (calciferol) metabolism / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of immune response proteins / SUMOylation of intracellular receptors / Formation of Incision Complex in GG-NER / condensed chromosome, centromeric region => GO:0000779 / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins ...Vitamin D (calciferol) metabolism / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of immune response proteins / SUMOylation of intracellular receptors / Formation of Incision Complex in GG-NER / condensed chromosome, centromeric region => GO:0000779 / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / pupariation / syncytial blastoderm mitotic cell cycle / SUMOylation of chromatin organization proteins / positive regulation of Toll signaling pathway / dorsal appendage formation / positive regulation of antimicrobial peptide production / central nervous system projection neuron axonogenesis / protein modification process => GO:0036211 / outer kinetochore / dendritic spine morphogenesis / positive regulation of smoothened signaling pathway / positive regulation of Ras protein signal transduction / ubiquitin-like protein ligase binding / lipid homeostasis / protein sumoylation / cellular response to transforming growth factor beta stimulus / mitotic spindle organization / condensed nuclear chromosome / positive regulation of protein localization to plasma membrane / positive regulation of MAP kinase activity / positive regulation of DNA-binding transcription factor activity / protein tag activity / midbody / nucleolus / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
Model detailsSolution Structure of SUMO-3 from Drosophila melanogaster (dsmt3)at 300K and pH 5.6
AuthorsKumar, D. / Misra, J.R. / Misra, A.K. / Chugh, J. / Sharma, S. / Hosur, R.V.
CitationJournal: Proteins / Year: 2009
Title: NMR-derived solution structure of SUMO from Drosophila melanogaster (dSmt3).
Authors: Kumar, D. / Misra, J.R. / Kumar, A. / Chugh, J. / Sharma, S. / Hosur, R.V.
History
DepositionMar 3, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG4494-PA


Theoretical massNumber of molelcules
Total (without water)9,9691
Polymers9,9691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein CG4494-PA / LD07775p / Smt3 / Ubiquitin-like protein SMT3


Mass: 9969.200 Da / Num. of mol.: 1 / Fragment: dsmt3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O97102

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution Structure of SUMO-3 from Drosophila melanogaster (dsmt3)at 300K and pH 5.6
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNHA
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D 1H-13C HSQC
1913D 1H-15N TOCSY
11013D CBCANH
11113D HNN
11213D HNCN
11313D (H)CC(CO)NH
NMR detailsText: The structure was determined using NOE.

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Sample preparation

DetailsContents: 100 mM sodium phosphate, 1 mM DTT, 150 mM sodium chloride, 1 mM EDTA, 10 % D2O, 90 % H2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium phosphate1
1 mMDTT1
150 mMsodium chloride1
1 mMEDTA1
10 %D2O1
90 %H2O1
Sample conditionsIonic strength: 0.1 / pH: 5.6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler, Wuthrichrefinement
CARA1.8Keller, Wuthrichpeak picking
CARA1.8Keller, Wuthrichchemical shift assignment
CARA1.8Keller, Wuthrichdata analysis
Felix2002Accelrys Software Inc.processing
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
Details: Uses Dihederal Angle Constraints and Noe restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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