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- PDB-6lag: Solution structure of SPA-2 SHD -

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Basic information

Entry
Database: PDB / ID: 6lag
TitleSolution structure of SPA-2 SHD
ComponentsSpa2-like protein
KeywordsSIGNALING PROTEIN / SHD / SPA-2 / GIT-PIX / polarity
Function / homologyProtein Spa2/Sph1 / cell cortex of growing cell tip / GIT, Spa2 homology (SHD) domain / Spa2 homology domain (SHD) of GIT / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / actomyosin contractile ring / MAP-kinase scaffold activity / Spa2-like protein
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsFan, J.S. / Wong, J.Y. / Zheng, P. / Yang, D. / Jedd, G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R-154-000-A50-114 Singapore
CitationJournal: Nat Commun / Year: 2020
Title: Spitzenkorper assembly mechanisms reveal conserved features of fungal and metazoan polarity scaffolds.
Authors: Zheng, P. / Nguyen, T.A. / Wong, J.Y. / Lee, M. / Nguyen, T.A. / Fan, J.S. / Yang, D. / Jedd, G.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spa2-like protein


Theoretical massNumber of molelcules
Total (without water)17,7821
Polymers17,7821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Spa2-like protein / SPA-2


Mass: 17781.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: spa2, NCU03115 / Production host: Escherichia coli (E. coli) / References: UniProt: V5IQM7

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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
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D (H)CCH-TOCSY
151isotropic14D NOESY

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Sample preparation

DetailsType: solution / Contents: 2 mM [U-13C; U-15N] SHD, 90% H2O/10% D2O / Label: 13C,15N_labeled sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: SHD / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 10 mM / Ionic strength err: 0.1 / Label: condition_1 / pH: 6.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: with cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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