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- PDB-5gjl: Solution structure of SUMO from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 5gjl
TitleSolution structure of SUMO from Plasmodium falciparum
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / SUMO
Function / homologyRad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Ubiquitin-like domain-containing protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / molecular dynamics
AuthorsSingh, J.S. / Shukla, V.K. / Gujrati, M. / Mishra, R.K. / Kumar, A.
CitationJournal: To Be Published
Title: Structure, dynamics and interaction study of SUMO from Plasmodium falciparum
Authors: Singh, J.S. / Shukla, V.K. / Gujrati, M. / Mishra, R.K. / Kumar, A.
History
DepositionJun 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,8391
Polymers10,8391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein / PfSUMO


Mass: 10838.997 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate Dd2) (eukaryote)
Strain: isolate Dd2 / Gene: PFDG_04583 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L7M5F7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D CBCA(CO)NH
132isotropic13D HN(CA)CB
142isotropic13D HNCO
152isotropic13D (H)CCH-TOCSY
162isotropic13D (H)CC(CO)NH
172isotropic13D CC(CO)NH
181isotropic23D 1H-15N NOESY
193isotropic23D 1H-13C NOESY aliphatic
1102isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O15N90% H2O/10% D2O
solution220 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O15N, 13C90% H2O/10% D2O
solution320 mM TRIS, 50 mM sodium chloride, 100% D2O15N, 13C100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance2
50 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance3
50 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 50 mM / Ionic strength err: 0.2 / Label: sample condition 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ASCENDBrukerASCEND7501
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CcpNMRCCPNchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: 1329 NOE and 136 dihedral angle
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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