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- PDB-7kbq: Solution NMR Structure of DE NOVO DESIGNED Rossmann 3x3 Fold Prot... -

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Entry
Database: PDB / ID: 7kbq
TitleSolution NMR Structure of DE NOVO DESIGNED Rossmann 3x3 Fold Protein r3x3_bp3, Northeast Structural Genomics Consortium (NESG) Target OR689
ComponentsDE NOVO DESIGNED OR689
KeywordsDE NOVO PROTEIN / Rossmann 3x3 fold / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, G. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
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
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: 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:
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Assembly

Deposited unit
A: DE NOVO DESIGNED OR689


Theoretical massNumber of molelcules
Total (without water)15,8231
Polymers15,8231
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 #1medoid

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Components

#1: Protein DE NOVO DESIGNED OR689


Mass: 15823.438 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
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D SIMUTANEOUS 1H, 15N, 13C NOESY
171isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-100% 13C; U-100% 15N] OR689, 90% H2O/10% D2O
Label: NC / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: OR689 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.peak picking
ASDPHuang, Montelionestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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