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- PDB-2m0m: Structural Characterization of Minor Ampullate Spidroin Domains a... -

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Basic information

Entry
Database: PDB / ID: 2m0m
TitleStructural Characterization of Minor Ampullate Spidroin Domains and their Distinct Roles in Fibroin Solubility and Fiber Formation
ComponentsMinor ampullate fibroin 1
KeywordsPROTEIN FIBRIL / Spider silk protein / MiSp1 / CTD / Dimer
Function / homology
Function and homology information


Spidroin domain, C-terminal domain / Tubuliform egg casing silk strands structural domain / Tubuliform egg casing silk strands structural domain / Spidroin, C-terminal / Spidroin, repetitive domain / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Minor ampullate fibroin 1
Similarity search - Component
Biological speciesNephila antipodiana (spider)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYang, D. / Gao, Z. / Lin, Z. / Huang, W. / Lai, C. / Fan, J.
CitationJournal: Plos One / Year: 2013
Title: Structural characterization of minor ampullate spidroin domains and their distinct roles in fibroin solubility and fiber formation
Authors: Gao, Z. / Lin, Z. / Huang, W. / Lai, C.C. / Fan, J.S. / Yang, D.
History
DepositionOct 30, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 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

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Assembly

Deposited unit
A: Minor ampullate fibroin 1
B: Minor ampullate fibroin 1


Theoretical massNumber of molelcules
Total (without water)21,0112
Polymers21,0112
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Minor ampullate fibroin 1


Mass: 10505.701 Da / Num. of mol.: 2 / Fragment: UNP residues 250-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2LC34

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1412D 1H-13C HSQC
1513D MQ-CCH-TOCSY
1614D 13C, 15N-edited NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] CTD-1, 10mM sodium phosphate-2, 0.01% sodium azide-3, 5mM EDTA-4, 50mM sodium chloride-5, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCTD-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
0.01 %sodium azide-31
5 mMEDTA-41
50 mMsodium chloride-51
Sample conditionsIonic strength: 0.06 / pH: 6.8 / Pressure: ambient / Temperature: 307 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
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxprocessing
NMRspyDaiwen Yang, Yu Zhengpeak picking
NMRspyDaiwen Yang, Yu Zhengchemical shift assignment
NMRspyDaiwen Yang, Yu Zhengnoe assignment
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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