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- PDB-2jvf: Solution structure of M7, a computationally-designed artificial p... -

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Basic information

Entry
Database: PDB / ID: 2jvf
TitleSolution structure of M7, a computationally-designed artificial protein
Componentsde novo protein M7
KeywordsDE NOVO PROTEIN / tetrapeptide fragment-based protein design / artificial fold
Function / homologytop7, de novo designed protein / top7, de novo designed protein / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesunidentified (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsStordeur, C. / Dalluege, R. / Birkenmeier, O. / Wienk, H. / Rudolph, R. / Lange, C. / Luecke, C.
Citation
Journal: Proteins / Year: 2008
Title: The NMR solution structure of the artificial protein M7 matches the computationally designed model
Authors: Stordeur, C. / Dalluege, R. / Birkenmeier, O. / Wienk, H. / Rudolph, R. / Lange, C. / Luecke, C.
#1: Journal: Proteins / Year: 2007
Title: A tetrapeptide fragment-based design method results in highly stable artificial proteins.
Authors: Dalluge, R. / Oschmann, J. / Birkenmeier, O. / Lucke, C. / Lilie, H. / Rudolph, R. / Lange, C.
History
DepositionSep 19, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999Sequence This is a de novo protein. The first four residues (GSHM) are cloning artifacts.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo protein M7


Theoretical massNumber of molelcules
Total (without water)10,8371
Polymers10,8371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein de novo protein M7


Mass: 10837.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pET-28a / 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-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-15N HSQC
1423D 1H-15N TOCSY-HSQC
1523D 1H-15N NOESY-HSQC
1622D 1H-15N HTQC
1732D 1H-1H TOCSY
1832D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM M7, 25 mM sodium phosphate, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.3 mM [U-98% 15N] M7, 25 mM sodium phosphate, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31.0 mM M7, 25 mM sodium phosphate, 0.05 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMM71
25 mMsodium phosphate1
0.05 %sodium azide1
1.3 mMM7[U-98% 15N]2
25 mMsodium phosphate2
0.05 %sodium azide2
1.0 mMM73
25 mMsodium phosphate3
0.05 %sodium azide3
Sample conditionsIonic strength: 25 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
Felix2000Accelrys Software Inc.data analysis
DYANA1.5Guntert, P. et al.structure solution
Discover2000Accelrys Software Inc.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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