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- PDB-2mtq: Solution Structure of a De Novo Designed Peptide that Sequesters ... -

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Basic information

Entry
Database: PDB / ID: 2mtq
TitleSolution Structure of a De Novo Designed Peptide that Sequesters Toxic Heavy Metals
ComponentsDesigned Peptide
KeywordsDE NOVO PROTEIN / De Novo Protein Design / Triscysteine / Three-helix bundle
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #130 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsPlegaria, J.S. / Zuiderweg, E.R. / Stemmler, T.L. / Pecoraro, V.L.
CitationJournal: Biochemistry / Year: 2015
Title: Apoprotein Structure and Metal Binding Characterization of a de Novo Designed Peptide, alpha 3DIV, that Sequesters Toxic Heavy Metals.
Authors: Plegaria, J.S. / Dzul, S.P. / Zuiderweg, E.R. / Stemmler, T.L. / Pecoraro, V.L.
History
DepositionAug 28, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 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: Designed Peptide


Theoretical massNumber of molelcules
Total (without water)8,0901
Polymers8,0901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Designed Peptide


Mass: 8090.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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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 HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D HNHA
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1912D 1H-13C HSQC
11013D 1H-15N NOESY
21123D 1H-13C NOESY aliphatic
21223D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium chloride, 0.5 % sodium azide, 0.05 mM PMSF, 0.8 mM TCEP, 1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
2100 mM sodium chloride, 0.5 % sodium azide, 0.05 mM PMSF, 0.8 mM TCEP, 1 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloride-11
0.5 %sodium azide-21
0.05 mMPMSF-31
0.8 mMTCEP-41
1 mMentity-5[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-62
0.5 %sodium azide-72
0.05 mMPMSF-82
0.8 mMTCEP-92
1 mMentity-10[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 7 ambient 298 K
2100 7 ambient 298 K

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NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / 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
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
narefinement
NMR constraintsHydrogen bond constraints total count: 78 / Protein chi angle constraints total count: 17 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 61
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.94 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.39 ° / Maximum upper distance constraint violation: 0.59 Å / Torsion angle constraint violation method: CYANA
NMR ensemble rmsDistance rms dev: 0.0128 Å / Distance rms dev error: 0.0014 Å

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