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- PDB-2mra: Solution NMR Structure of De novo designed protein, Northeast Str... -

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Basic information

Entry
Database: PDB / ID: 2mra
TitleSolution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR459
ComponentsDe novo designed protein OR459
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 / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsPulavarti, S.V.S.R.K. / Kipnis, Y. / Sukumaran, D. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. ...Pulavarti, S.V.S.R.K. / Kipnis, Y. / Sukumaran, D. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR459
Authors: Pulavarti, S.V.S.R.K. / Kipnis, Y. / Sukumaran, D. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. / Szyperski, T.
History
DepositionJul 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: De novo designed protein OR459


Theoretical massNumber of molelcules
Total (without water)13,4061
Polymers13,4061
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein De novo designed protein OR459


Mass: 13406.320 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-COSY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D HN(CA)CO
1111GFT-4,3d-(H)CCH-COSY
11212D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 1.17 mM OR459.005, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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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
CARARochus Kelleranalysis
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1 / Details: Water bath refinement
NMR constraintsNOE constraints total: 1572 / NOE intraresidue total count: 227 / NOE long range total count: 535 / NOE medium range total count: 389 / NOE sequential total count: 421 / Protein phi angle constraints total count: 153 / Protein psi angle constraints total count: 153
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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