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- PDB-6qf8: Solution NMR ensemble for human ubiquitin at 298K compiled using ... -

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Basic information

Entry
Database: PDB / ID: 6qf8
TitleSolution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method
ComponentsPolyubiquitin-B
KeywordsSIGNALING PROTEIN / CoMAND method / R-factor refinement
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin B / Tail fiber
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / R-factor based frame picking
AuthorsElGamacy, M. / Truffault, V. / Zhu, H. / Coles, M.
CitationJournal: Structure / Year: 2019
Title: Mapping Local Conformational Landscapes of Proteins in Solution.
Authors: ElGamacy, M. / Riss, M. / Zhu, H. / Truffault, V. / Coles, M.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_software.name
Revision 1.2May 15, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)8,8361
Polymers8,8361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4900 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000NOESY-based R-factor selection
RepresentativeModel #1closest to the average

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Components

#1: Protein Polyubiquitin-B


Mass: 8836.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D CNH-NOESY
121isotropic33D C(CO)NH

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate, 95% H2O/5% D2O
Label: double_labelled / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhuman ubiquitin[U-99% 13C; U-99% 15N]1
40 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 5.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
Rosetta3.6Das & Bakerstructure calculation
NAMD 2.12University of Illinoisrefinement
ShineRiss & Colesrefinement
CoMANDin houserefinement
RefinementMethod: R-factor based frame picking / Software ordinal: 5
Details: frames selected from unrestrained MD simulations to minimise the overall NOESY-based R-factor
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: NOESY-based R-factor selection
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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