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- PDB-2lyi: Repetitive domain (RP) of aciniform spidroin 1 from Nephila antip... -

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Basic information

Entry
Database: PDB / ID: 2lyi
TitleRepetitive domain (RP) of aciniform spidroin 1 from Nephila antipodiana
ComponentsPROTEIN (entity)
KeywordsSTRUCTURAL PROTEIN / PROTEIN
Function / homologySpidroin, repetitive domain / Spidroin, repetitive domain / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha / PROTEIN (entity)
Function and homology information
Biological speciesNephila antipodiana (spider)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsWang, S. / Huang, W. / Yang, D.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: NMR structure note: repetitive domain of aciniform spidroin 1 from Nephila antipodiana
Authors: Wang, S. / Huang, W. / Yang, D.
History
DepositionSep 18, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: 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 / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
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: PROTEIN (entity)


Theoretical massNumber of molelcules
Total (without water)17,0791
Polymers17,0791
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein PROTEIN (entity)


Mass: 17079.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1E5*PLUS
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1714D time shared 13C/15N-edited NOESY

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Sample preparation

DetailsContents: 2mM [U-100% 13C; U-100% 15N]AcSp1-RP-1, 95%H2O/5%D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 2 mM / Component: AcSp1-RP-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRspyYu Zheng, Daiwen Yangchemical shift assignment
TopSpinBruker Biospincollection
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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