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- PDB-2kc5: Solution Structure of HybE from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2kc5
TitleSolution Structure of HybE from Escherichia coli
ComponentsHydrogenase-2 operon protein hybE
KeywordsCHAPERONE
Function / homology
Function and homology information


preprotein binding / protein maturation
Similarity search - Function
[NiFe]-hydrogenase assembly chaperone, HybE / [NiFe]-hydrogenase assembly, chaperone, HybE / [NiFe]-hydrogenase assembly chaperone, HybE superfamily / [NiFe]-hydrogenase assembly, chaperone, HybE / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase-2 operon protein HybE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsJin, C. / Shao, X. / Lu, J. / Li, Y.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of the Escherichia coli HybE reveals a novel fold
Authors: Shao, X. / Lu, J. / Hu, Y. / Xia, B. / Jin, C.
History
DepositionDec 17, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase-2 operon protein hybE


Theoretical massNumber of molelcules
Total (without water)17,9801
Polymers17,9801
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 Hydrogenase-2 operon protein hybE


Mass: 17979.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: hybE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AAN1

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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
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D (H)CCH-COSY
1713D HNCO
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-99% 15N] 50mM NaCl, 50mM PBS-1, 1mM [U-99% 13C; U-99% 15N] 50mM NaCl, 50mM PBS-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM50mM NaCl, 50 mM PBS-1[U-99% 15N]1
1 mM50mM NaCl, 50 mM PBS-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 4243 / NOE intraresidue total count: 625 / NOE long range total count: 2506 / NOE medium range total count: 539 / NOE sequential total count: 249
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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