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- PDB-2mrc: NMR Structure and 1H, 13C and 15N Chemical Shift Assignments for ... -

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Basic information

Entry
Database: PDB / ID: 2mrc
TitleNMR Structure and 1H, 13C and 15N Chemical Shift Assignments for High mobility group protein from Plasmodium falciparum 3D7.
ComponentsHigh mobility group protein
KeywordsPROTEIN BINDING / pathogenesis / virulence / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


positive regulation of cytokine production involved in immune response / chromatin => GO:0000785 / regulation of transcription by RNA polymerase III / DNA binding, bending / chromosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / cytosol
Similarity search - Function
HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
High mobility group protein B2
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, C. / Barnwal, R. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: NMR Structure and 1H, 13C and 15N Chemical Shift Assignments for High mobility group protein from Plasmodium falciparum 3D7.
Authors: Tang, C. / Barnwal, R. / Varani, G.
History
DepositionJul 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: High mobility group protein


Theoretical massNumber of molelcules
Total (without water)10,8621
Polymers10,8621
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)10 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein High mobility group protein


Mass: 10861.688 Da / Num. of mol.: 1 / Fragment: unp residues 17-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PfHMGB2, MAL8P1.72 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IB14

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D C(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D HNHA

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Sample preparation

DetailsContents: 0.9 mM [U-95% 13C; U-95% 15N] High mobility group protein, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 0.9 mM / Component: High mobility group protein-1 / Isotopic labeling: [U-95% 13C; U-95% 15N]
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CCPNMRCCPNdata analysis
CCPNMRCCPNchemical shift assignment
CCPNMRCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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