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- PDB-2jws: Solution NMR structures of two designed proteins with 88% sequenc... -

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Basic information

Entry
Database: PDB / ID: 2jws
TitleSolution NMR structures of two designed proteins with 88% sequence identity but different fold and function
ComponentsGa88
KeywordsDE NOVO PROTEIN / evolution / folding / protein design
Function / homologyAlbumin-binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailssolution structure of Ga88
AuthorsHe, Y. / Chen, Y. / Alexander, P. / Bryan, P. / Orban, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: NMR structures of two designed proteins with high sequence identity but different fold and function
Authors: He, Y. / Chen, Y. / Alexander, P. / Bryan, P.N. / Orban, J.
History
DepositionOct 24, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_keywords.text
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ga88


Theoretical massNumber of molelcules
Total (without water)6,3171
Polymers6,3171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Ga88


Mass: 6317.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: PGA88 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: solution structure of Ga88
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: 02~0.4 mM [U-100% 13C; U-100% 15N] Ga88, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 02 mM / Component: Ga88 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 295 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
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XwinNMR2.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddarddata analysis
CNS1.1Brunger, 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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