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- PDB-6xeh: Solution NMR Structure of DE NOVO DESIGNED Rossmann 2x3 Fold Prot... -

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Basic information

Entry
Database: PDB / ID: 6xeh
TitleSolution NMR Structure of DE NOVO DESIGNED Rossmann 2x3 Fold Protein r2x3_168, Northeast Structural Genomics Consortium (NESG) Target OR386
ComponentsDE NOVO DESIGNED OR386
KeywordsDE NOVO PROTEIN / Rosemann 2x3 fold NMR / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyRossmann fold - #11230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsLiu, G. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Role of backbone strain in de novo design of complex alpha/beta protein structures Accurate de novo design of asymetric alpha/beta proteins with ten or more secondary structure elements ...Title: Role of backbone strain in de novo design of complex alpha/beta protein structures Accurate de novo design of asymetric alpha/beta proteins with ten or more secondary structure elements requires consideration of backbone strain Design principle proposed from designed larger alpha/beta-proteins not folded as designed: Consistency between local, non-local, and global structures
Authors: Koga, N. / Koga, R. / Liu, G. / Castellanos, J. / Montelione, G.T. / Baker, D.
History
DepositionJun 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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: DE NOVO DESIGNED OR386


Theoretical massNumber of molelcules
Total (without water)14,5351
Polymers14,5351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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 DESIGNED OR386


Mass: 14535.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D SIMUTANEOUS 1H, 15N, 13C NOESY
192isotropic12D 1H-13C HSQC aliphatic
1103anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.6 mM [U-13C; U-15N] OR386, 90% H2O/10% D2ONC90% H2O/10% D2O
solution30.6 mM [U-10% 13C; U-100% 15N] OR386, 90% H2O/10% D2ONC5_rdc90% H2O/10% D2ORDC measurement
solution20.6 mM [U-10% 13C; U-100% 15N] OR386, 90% H2O/10% D2ONC590% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMOR386[U-13C; U-15N]1
0.6 mMOR386[U-10% 13C; U-100% 15N]3
0.6 mMOR386[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ASDPHuang, Montelionestructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinal
simulated annealing1
torsion angle dynamics2
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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