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- PDB-2mbl: Solution NMR Structure of De novo designed Top7 Fold Protein Top7... -

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Basic information

Entry
Database: PDB / ID: 2mbl
TitleSolution NMR Structure of De novo designed Top7 Fold Protein Top7m13, Northeast Structural Genomics Consortium (NESG) Target OR33
ComponentsTop7 Fold Protein Top7m13
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologytop7, de novo designed protein / top7, de novo designed protein / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / distance geometry, molecular dynamics, simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsLiu, G. / Zanghellini, A.L. / Chan, K. / Xiao, R. / Janjua, H. / Kogan, S. / Maglaqui, M. / Ciccosanti, C. / Acton, T.B. / Kornhaber, G. ...Liu, G. / Zanghellini, A.L. / Chan, K. / Xiao, R. / Janjua, H. / Kogan, S. / Maglaqui, M. / Ciccosanti, C. / Acton, T.B. / Kornhaber, G. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of De novo designed Top7 Fold Protein Top7m13, Northeast Structural Genomics Consortium (NESG) Target OR33
Authors: Liu, G. / Zanghellini, A.L. / Chan, K. / Xiao, R. / Janjua, H. / Kogan, S. / Maglaqui, M. / Ciccosanti, C. / Acton, T.B. / Kornhaber, G. / Everett, J.K. / Baker, D. / Montelione, G.T.
History
DepositionAug 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Top7 Fold Protein Top7m13


Theoretical massNumber of molelcules
Total (without water)13,8881
Polymers13,8881
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Top7 Fold Protein Top7m13


Mass: 13887.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The final structures were refined in explicit water using the program CNS with 2747 conformationally restricting constraints and addtional 67 RDC constraints. This final structure were ...Details: The final structures were refined in explicit water using the program CNS with 2747 conformationally restricting constraints and addtional 67 RDC constraints. This final structure were further refined by using restained Rosetta (http://psvs-1_4-dev.nesg.org/consRosetta.html) with the same constraints, the refined coordinated is deposited to PDB with PDB ID 2MBM, which shows better Procheck and MolProbity quality score but with higher restraint violations.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D (H)CCH-TOCSY
1922D 1H-13C HSQC aliphatic
11032D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.69 mM [U-100% 13C; U-100% 15N] OR33.017, 90% H2O/10% D2O90% H2O/10% D2O
20.69 mM [U-100% 13C; U-100% 15N] OR33.007, 90% H2O/10% D2O90% H2O/10% D2O
30.69 mM [U-100% 13C; U-100% 15N] OR33.007_rdc, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.69 mMOR33.017-1[U-100% 13C; U-100% 15N]1
0.69 mMOR33.007-2[U-100% 13C; U-100% 15N]2
0.69 mMOR33.007_rdc-3[U-100% 13C; U-100% 15N]3
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: distance geometry, molecular dynamics, simulated annealing, 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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