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- PDB-2l82: Solution NMR Structure of de novo designed protein, P-loop NTPase... -

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Basic information

Entry
Database: PDB / ID: 2l82
TitleSolution NMR Structure of de novo designed protein, P-loop NTPase fold, Northeast Structural Genomics Consortium Target OR32
ComponentsDESIGNED PROTEIN OR32
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, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Janjua, H. / Tong, S. / Acton, T.B. / Everett, J. / Baker, D. ...Liu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Janjua, H. / Tong, S. / Acton, T.B. / Everett, J. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR32
Authors: Liu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Janjua, H. / Tong, S. / Acton, T.B. / Everett, J. / Baker, D. / Montelione, G.T.
History
DepositionDec 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 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
Revision 1.3May 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: DESIGNED PROTEIN OR32


Theoretical massNumber of molelcules
Total (without water)19,7011
Polymers19,7011
Non-polymers00
Water00
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 DESIGNED PROTEIN OR32


Mass: 19701.045 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 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

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Sample preparation

Details
Solution-IDContentsSolvent system
11.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O90% H2O/10% D2O
20.85 mM [U-5% 13C; U-100% 15N] OR32, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.06 mMOR32-1[U-100% 13C; U-100% 15N]1
0.85 mMOR32-2[U-5% 13C; U-100% 15N]2
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

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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
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
CYANArefinement
CNSrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
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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