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- PDB-2kdm: NMR structures of GA95 and GB95, two designed proteins with 95% s... -

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Basic information

Entry
Database: PDB / ID: 2kdm
TitleNMR structures of GA95 and GB95, two designed proteins with 95% sequence identity but different folds and functions
ComponentsDESIGNED PROTEIN
KeywordsIgG binding protein / evolution / folding / protein design
Function / homologyUbiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsHe, Y. / Alexander, P. / Chen, Y. / Bryan, P. / Orban, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: A minimal sequence code for switching protein structure and function.
Authors: Alexander, P.A. / He, Y. / Chen, Y. / Orban, J. / Bryan, P.N.
History
DepositionJan 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DESIGNED PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,3631
Polymers6,3631
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 / 300structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein DESIGNED PROTEIN


Mass: 6363.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: designed protein

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D HNCO
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.15-0.3 mM [U-100% 13C; U-100% 15N] Gb95, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: Gb95 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.15-0.3
Sample conditionsIonic strength: 100 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XwinNMR2.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddarddata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 20

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