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- PDB-2mu3: Spider wrapping silk fibre architecture arising from its modular ... -

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Basic information

Entry
Database: PDB / ID: 2mu3
TitleSpider wrapping silk fibre architecture arising from its modular soluble protein precursor
ComponentsAciniform spidroin 1
KeywordsSTRUCTURAL PROTEIN / spider silk / W1 / wrapping silk / AcSp1 / aciniform spidroin
Function / homologyTubuliform 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 / Aciniform spidroin 1
Function and homology information
Biological speciesArgiope trifasciata (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsXu, L. / Tremblay, M. / Meng, Q. / Liu, X. / Rainey, J.K. / Lefevre, T. / Sarker, M. / Orrell, K.E. / Leclerc, J. / Pezolet, M. / Auger, M.
Citation
Journal: Sci Rep / Year: 2015
Title: Spider wrapping silk fibre architecture arising from its modular soluble protein precursor.
Authors: Tremblay, M.L. / Xu, L. / Lefevre, T. / Sarker, M. / Orrell, K.E. / Leclerc, J. / Meng, Q. / Pezolet, M. / Auger, M. / Liu, X.Q. / Rainey, J.K.
#1: Journal: Biomol.Nmr Assign. / Year: 2012
Title: 1H, 13C and 15N NMR assignments of the aciniform spidroin (AcSp1) repetitive domain of Argiope trifasciata wrapping silk.
Authors: Xu, L. / Tremblay, M.L. / Meng, Q. / Liu, X.Q. / Rainey, J.K.
History
DepositionSep 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: 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: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)18,9811
Polymers18,9811
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aciniform spidroin 1


Mass: 18981.467 Da / Num. of mol.: 1 / Fragment: W1 repeating domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argiope trifasciata (spider) / Organ: Aciniform gland / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64K55

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1213D HNCO
1313D HN(CA)CB
1413D HNCA
151HN(CA)CO (H[N[ca[CO]]])
161HN(CO)CA (H[N[co[{CA|ca[C]}]]])
1713D HNHB
181HNHA (H{[N]+[HA]})
191ChHN (h[C] H[N].through-space)
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY aromatic
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D HNHB
11512D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.76 mM [U-100% 13C; U-100% 15N] W1, 1 mM DSS, 1 mM sodium azide, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.76 mMW1-1[U-100% 13C; U-100% 15N]1
1 mMDSS-21
1 mMsodium azide-31
20 mMsodium acetate-4[U-2H]1
Sample conditionsIonic strength: 0.100 / pH: 5.020 / Pressure: 1.000 atm / Temperature: 303.150 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.1CCPNdata analysis
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNpeak picking
CcpNmr Analysis2.1Linge, O'Donoghue and Nilgesdata analysis
CcpNmr Analysis2.1Linge, O'Donoghue and Nilgeschemical shift assignment
CcpNmr Analysis2.1Linge, O'Donoghue and Nilgespeak picking
NMRPipe1Dr. Delaglio and Dr. Baxdata processing
NMRPipe1Dr. Delaglio and Dr. Baxrefinement
NMRPipe1Schwieters, Kuszewski, Tjandra and Cloredata processing
NMRPipe1Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe1Cornilescu, Delaglio and Baxdata processing
NMRPipe1Cornilescu, Delaglio and Baxrefinement
NMRPipe1Dr. Delaglio and Dr. Baxdata processing
NMRPipe1Dr. Delaglio and Dr. Baxrefinement
NMRPipe1Schwieters, Kuszewski, Tjandra and Cloredata processing
NMRPipe1Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe1Cornilescu, Delaglio and Baxdata processing
NMRPipe1Cornilescu, Delaglio and Baxrefinement
ARIA2Linge, O'Donoghue and Nilgesrefinement
ARIA2Linge, O'Donoghue and Nilgesstructure solution
X-PLOR NIHrefinement
RefinementMethod: torsion angle dynamics / 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: 20 / Representative conformer: 1

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