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- PDB-6dri: NMR solution structure of Acan1 from the Ancylostoma caninum hookworm -

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Basic information

Entry
Database: PDB / ID: 6dri
TitleNMR solution structure of Acan1 from the Ancylostoma caninum hookworm
ComponentsAcan1
KeywordsIMMUNE SYSTEM / DISULFIDE-RICH PEPTIDE
Function / homologyShK domain-like / ShKT domain / ShKT domain profile. / ShKT domain-containing protein
Function and homology information
Biological speciesAncylostoma caninum (dog hookworm)
MethodSOLUTION NMR / simulated annealing
AuthorsSmallwood, T.B. / Rosengren, K.J. / Clark, R.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT100100476 Australia
CitationJournal: To Be Published
Title: NMR solution structure of Acan1 from the Ancylostoma caninum hookworm
Authors: Smallwood, T.B. / Rosengren, K.J. / Clak, R.J.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acan1


Theoretical massNumber of molelcules
Total (without water)4,6411
Polymers4,6411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint0 kcal/mol
Surface area3190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Acan1


Mass: 4641.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ancylostoma caninum (dog hookworm) / References: UniProt: A0A368FHQ4*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D DQF-COSY
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mg/mL Acan1, 90% H2O/10% D2O / Label: Acan1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mg/mL / Component: Acan1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: NA Not defined / Label: condition_1 / pH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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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
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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