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- PDB-2n7p: Solution structure of PDZ domain -

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Basic information

Entry
Database: PDB / ID: 2n7p
TitleSolution structure of PDZ domain
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / PDZ
Function / homology
Function and homology information


cullin-RING ubiquitin ligase complex / ciliary basal body / nucleolus
Similarity search - Function
PDZ superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMei, S.
CitationJournal: To be Published
Title: Solution structure of Q388A3 PDZ domain from Trypanosoma brucei and its interaction with OMP-like peptide
Authors: Mei, S.
History
DepositionSep 17, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 7, 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 / 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 / _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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,9851
Polymers10,9851
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)20 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein


Mass: 10985.445 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1528-1630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.61.1430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q388A3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 100 mM sodium chloride-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 100 mM / Component: sodium chloride-1
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 20 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
PyMOLrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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