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- PDB-2mfz: NMR structure of C-terminal domain from A. ventricosus minor ampu... -

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Basic information

Entry
Database: PDB / ID: 2mfz
TitleNMR structure of C-terminal domain from A. ventricosus minor ampullate spidroin (MiSp)
ComponentsMinor ampullate spidroin
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Spidroin domain, C-terminal domain / Spidroin, C-terminal / Spidroin, repetitive domain / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Minor ampullate spidroin
Similarity search - Component
Biological speciesAraneus ventricosus (diadem spider)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsOtikovs, M. / Jaudzems, K. / Andersson, M. / Chen, G. / Landreh, M. / Nordling, K. / Kronqvist, N. / Westermark, P. / Jornvall, H. / Knight, S. ...Otikovs, M. / Jaudzems, K. / Andersson, M. / Chen, G. / Landreh, M. / Nordling, K. / Kronqvist, N. / Westermark, P. / Jornvall, H. / Knight, S. / Ridderstrale, Y. / Holm, L. / Meng, Q. / Chesler, M. / Johansson, J. / Rising, A.
CitationJournal: Plos Biol. / Year: 2014
Title: Carbonic Anhydrase Generates CO2 and H+ That Drive Spider Silk Formation Via Opposite Effects on the Terminal Domains
Authors: Andersson, M. / Chen, G. / Otikovs, M. / Landreh, M. / Nordling, K. / Kronqvist, N. / Westermark, P. / Jornvall, H. / Knight, S. / Ridderstrale, Y. / Holm, L. / Meng, Q. / Jaudzems, K. / ...Authors: Andersson, M. / Chen, G. / Otikovs, M. / Landreh, M. / Nordling, K. / Kronqvist, N. / Westermark, P. / Jornvall, H. / Knight, S. / Ridderstrale, Y. / Holm, L. / Meng, Q. / Jaudzems, K. / Chesler, M. / Johansson, J. / Rising, A.
History
DepositionOct 24, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor ampullate spidroin
B: Minor ampullate spidroin


Theoretical massNumber of molelcules
Total (without water)23,5342
Polymers23,5342
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Minor ampullate spidroin


Mass: 11766.801 Da / Num. of mol.: 2 / Fragment: UNP residues 1647-1766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Araneus ventricosus (diadem spider)
Description: His tag-Thioredoxin-His tag followed by a thrombin cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K4MTL7

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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 CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1923D 13C,15N filtered 1H-13C NOESY aliphatic
11022D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContents
11 mM [U-99% 13C; U-99% 15N] Minor ampullate spidroin CT-1, 20 mM sodium phosphate-2, 20 mM sodium chloride-3, 0.03 % sodium azide-4, 8 % [U-100% 2H] D2O-5, 92% H2O/8% D2O
20.25 mM [U-99% 13C; U-99% 15N] Minor ampullate spidroin CT-6, 0.25 mM Minor ampullate spidroin CT-7, 20 mM sodium phosphate-8, 20 mM sodium chloride-9, 0.03 % sodium azide-10, 8 % [U-100% 2H] D2O-11, 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMinor ampullate spidroin CT-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
20 mMsodium chloride-31
0.03 %sodium azide-41
8 %D2O-5[U-100% 2H]1
0.25 mMMinor ampullate spidroin CT-6[U-99% 13C; U-99% 15N]2
0.25 mMMinor ampullate spidroin CT-72
20 mMsodium phosphate-82
20 mMsodium chloride-92
0.03 %sodium azide-102
8 %D2O-11[U-100% 2H]2
Sample conditionsIonic strength: 0.0688 / pH: 6.8 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
UNIOT. Herrmann, F. Fiorito, J. Volkpeak picking
VnmrJVariancollection
TopSpinBruker Biospinprocessing
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Used for structure refinement, Used for structure calculation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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