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- PDB-2lhd: GB98 solution structure -

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Basic information

Entry
Database: PDB / ID: 2lhd
TitleGB98 solution structure
ComponentsGB98
KeywordsDE NOVO PROTEIN
Function / homologyUbiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHe, Y. / Chen, Y. / Alexander, P. / Bryan, P. / Orban, J.
CitationJournal: Structure / Year: 2012
Title: Mutational tipping points for switching protein folds and functions.
Authors: He, Y. / Chen, Y. / Alexander, P.A. / Bryan, P.N. / Orban, J.
History
DepositionAug 8, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: 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
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GB98


Theoretical massNumber of molelcules
Total (without water)6,4051
Polymers6,4051
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 / 500structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein GB98


Mass: 6405.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Gene: PGB98 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D C(CO)NH
1513D HNCO
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D H(CCO)NH
11013D HBHA(CO)NH

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Sample preparation

DetailsContents: 0.1-0.3 mM [U-100% 13C; U-100% 15N] GB98, 100 mM potassium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMGB98-1[U-100% 13C; U-100% 15N]0.1-0.31
100 mMpotassium phosphate-21
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.structure determination
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata processing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata processing display
SparkyGoddarddata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure display
CSIWishart, D.S. and B.D. Sykes.secondary structure prediction
TALOSCornilescu, Delaglio and Baxdihedral angle restraints determination
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thoprotein structure quality check
NOEIDLisa Parsonsgenerate noe peak lists
CNSBrunger A. T. et.al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 648 / NOE intraresidue total count: 395 / NOE long range total count: 91 / NOE medium range total count: 43 / NOE sequential total count: 119
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 500 / Conformers submitted total number: 20

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