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- PDB-2hfd: NMR structure of protein Hydrogenase-1 operon protein hyaE from E... -

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Basic information

Entry
Database: PDB / ID: 2hfd
TitleNMR structure of protein Hydrogenase-1 operon protein hyaE from Escherichia coli: Northeast Structural Genomics Consortium Target ER415
ComponentsHydrogenase-1 operon protein hyaE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE / NESGC / ALFA-BETA / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology[NiFe]-hydrogenase maturation factor HyaE / Hydrogenase-1 expression protein HyaE / signal sequence binding / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Hydrogenase-1 operon protein HyaE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsSingarapu, K.K. / Liu, G. / Eletsky, A. / Parish, D. / Atreya, H.S. / Xu, D. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. ...Singarapu, K.K. / Liu, G. / Eletsky, A. / Parish, D. / Atreya, H.S. / Xu, D. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2008
Title: Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif.
Authors: Parish, D. / Benach, J. / Liu, G. / Singarapu, K.K. / Xiao, R. / Acton, T. / Su, M. / Bansal, S. / Prestegard, J.H. / Hunt, J. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase-1 operon protein hyaE


Theoretical massNumber of molelcules
Total (without water)15,9731
Polymers15,9731
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hydrogenase-1 operon protein hyaE


Mass: 15972.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL-10 / Gene: hyaE / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P19931

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D (H)CCH-COSY
1513D 13C-separated NOESY
1613D 15N-separated NOESY
1713D aro NOESY

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Sample preparation

DetailsContents: 0.6mM Protein Hydrogenase-1 Operon Protein hyaE; 0.02% NaN3, 100mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2004.061.12.44Delaglio et alprocessing
DYANA1.5GUNTERT et aldata analysis
CYANA2.1GUNTERT et alrefinement
AUTOSTRUCTURE2.0.0HUANG et aldata analysis
CYANA1.5GUNTERT et aldata analysis
CNS1.1BRUNGER et alrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 1996 restraints, 1523 are NOE-derived distance constraints, 473 dihedral angle restraints,
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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