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- PDB-2kpo: Solution NMR structure of de novo designed rossmann 2x2 fold prot... -

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Basic information

Entry
Database: PDB / ID: 2kpo
TitleSolution NMR structure of de novo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium target OR16
Componentsrossmann 2x2 fold protein
KeywordsDE NOVO PROTEIN / De Novo Designed / Rossmann fold / NESG / GFT NMR / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
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, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Koga, R. / Koga, N. / Xiao, R. / Hamilton, K. / Ciccosanti, C. / Acton, T.B. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of denovo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium target OR16
Authors: Liu, G. / Koga, R. / Koga, N. / Baker, D. / Montelione, G.T.
History
DepositionOct 17, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2012Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 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 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)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D H(CCO)NH
161GFT (4,3)D HABCAB(CO)NHN
171SIMUTANEOUS 1H, 15N, 13C NOESY
1813D CCHTOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.859 mM [U-100% 13C; U-100% 15N] protein, 93% H2O/7% D2O93% H2O/7% D2O
20.867 mM [U-10% 13C; U-100% 15N] protein, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.859 mMprotein-1[U-100% 13C; U-100% 15N]1
0.867 mMprotein-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionedata analysis
AutoStructureHuang, Tejero, Powers and Montelionegeometry optimization
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRJVariancollection
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, 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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