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- PDB-2n3e: Amino-terminal domain of Latrodectus hesperus MaSp1 with neutrali... -

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Basic information

Entry
Database: PDB / ID: 2n3e
TitleAmino-terminal domain of Latrodectus hesperus MaSp1 with neutralized acidic cluster
ComponentsMajor ampullate spidroin 1
KeywordsSTRUCTURAL PROTEIN / five-helix bundle
Function / homology
Function and homology information


Spidroin, C-terminal / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Spidroin, N-terminal domain / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Major ampullate spidroin 1
Similarity search - Component
Biological speciesLatrodectus hesperus (western black widow)
MethodSOLUTION NMR / simulated annealing
AuthorsSchaal, D. / Bauer, J. / Schweimer, K. / Scheibel, T. / Roesch, P. / Schwarzinger, S.
CitationJournal: To be Published
Title: High resolution structure of an engineered amino-terminal ampullate spider silk with neutralized charge cluster
Authors: Schaal, D. / Bauer, J. / Schweimer, K. / Scheibel, T. / Roesch, P. / Schwarzinger, S.
History
DepositionMay 29, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: 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 / 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 / _pdbx_nmr_spectrometer.model / _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: Major ampullate spidroin 1


Theoretical massNumber of molelcules
Total (without water)14,0111
Polymers14,0111
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 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major ampullate spidroin 1


Mass: 14011.478 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 25-157) / Mutation: D39N, E76Q, E81Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Latrodectus hesperus (western black widow)
Gene: MaSp1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6YIY1
Sequence detailsAUTHORS STATE THAT THIS IS A CLONING OVERLAP

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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-15N HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D HNCA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D 1H-13C NOESY aromatic
11113D CCH-NOESY

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Sample preparation

DetailsContents: 600 uM [U-95% 13C; U-90% 15N] protein, 20 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMprotein-1[U-95% 13C; U-90% 15N]1
20 mMsodium phosphate-21
Sample conditionsIonic strength: 20 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance II+BrukerAVANCE II6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH1.2.1Schwieters, Kuszewski, Tjandra and Clorestructure solution
CcpNmr Analysis2.4Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauechemical shift assignment
CcpNmr Analysis2.4Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauepeak picking
CcpNmr Analysis2.4Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauedata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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