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- PDB-2lv8: Solution NMR Structure de novo designed rossmann 2x2 fold protein... -

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Basic information

Entry
Database: PDB / ID: 2lv8
TitleSolution NMR Structure de novo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium (NESG) Target OR16
ComponentsDe novo designed rossmann 2x2 fold protein
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologyRossmann fold - #11230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Koga, R. / Koga, N. / Xiao, R. / Pederson, K. / Hamilton, K. / Ciccosanti, C. / Acton, T.B. / Everett, J.K. / Baker, D. ...Liu, G. / Koga, R. / Koga, N. / Xiao, R. / Pederson, K. / Hamilton, K. / Ciccosanti, C. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nature / Year: 2012
Title: Principles for designing ideal protein structures.
Authors: Koga, N. / Tatsumi-Koga, R. / Liu, G. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionJun 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Jan 23, 2013Group: Database references
Revision 1.4Jun 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

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Assembly

Deposited unit
A: De novo designed rossmann 2x2 fold protein


Theoretical massNumber of molelcules
Total (without water)13,0781
Polymers13,0781
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 De novo designed rossmann 2x2 fold protein


Mass: 13077.996 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: NMR structure refined with RDC data
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 C(CO)NH
1913D (H)CCH-TOCSY
11022D 1H-13C HSQC
11132D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.073 mM [U-100% 13C; U-100% 15N] OR16.004, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.867 mM [U-100% 13C; U-100% 15N] OR16.006, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.859 mM [U-100% 13C; U-100% 15N] OR16.013, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.073 mMOR16.004-1[U-100% 13C; U-100% 15N]1
1 %Proteinase Inhibitors-21
0.02 %NaN3-31
10 mMDTT-41
5 mMCaCL2-51
200 mMNaCL-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
0.867 mMOR16.006-10[U-100% 13C; U-100% 15N]2
1 %Proteinase Inhibitors-112
0.02 %NaN3-122
10 mMDTT-132
5 mMCaCL2-142
200 mMNaCL-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
0.859 mMOR16.013-19[U-100% 13C; U-100% 15N]3
1 %Proteinase Inhibitors-203
0.02 %NaN3-213
10 mMDTT-223
5 mMCaCL2-233
200 mMNaCL-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
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
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
PSVSBhattacharya, Montelionestructure validation
PSVSBhattacharya, Montelionerefinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics, molecular 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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