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- PDB-2auv: Solution Structure of HndAc : A Thioredoxin-like [2Fe-2S] Ferredo... -

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Basic information

Entry
Database: PDB / ID: 2auv
TitleSolution Structure of HndAc : A Thioredoxin-like [2Fe-2S] Ferredoxin Involved in the NADP-reducing Hydrogenase Complex
Componentspotential NAD-reducing hydrogenase subunit
KeywordsOXIDOREDUCTASE / thioredoxin / thiordoxin-like
Function / homology
Function and homology information


hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / NADP-reducing hydrogenase subunit HndA
Similarity search - Component
Biological speciesDesulfovibrio fructosovorans (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNouailler, M. / Morelli, X. / Bornet, O. / Chetrit, B. / Dermoun, Z. / Guerlesquin, F.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex
Authors: Nouailler, M. / Morelli, X. / Bornet, O. / Chetrit, B. / Dermoun, Z. / Guerlesquin, F.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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: potential NAD-reducing hydrogenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2622
Polymers9,0861
Non-polymers1761
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein potential NAD-reducing hydrogenase subunit


Mass: 9085.789 Da / Num. of mol.: 1 / Fragment: Subunit A c-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio fructosovorans (bacteria)
Plasmid: pET-hndAc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q46505, hydrogen dehydrogenase (NADP+)
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1433D 15N-separated NOESY
1533D 15N-separated TOCSY
164HNCA-J
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and 2D/3D heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM oxidized HndAc, 10mM Sodium phosphate buffer (pH 6.0), 100mM NaCl90% H2O/10% D2O
21mM oxidized HndAc99% D2O
31mM oxidized HndAc U-15N, 10mM Sodium phosphate buffer (pH 6.0), 100mM NaCl90% H2O/10% D2O
40.15mM oxidized HndAc U-15N,13c, 10mM Sodium phosphate buffer (pH 6.0), 100mM NaCl90% H2O/10% D2O
Sample conditionsIonic strength: 10mM Sodium phosphate buffer, 100mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3brukercollection
XwinNMR3brukerprocessing
Felix2002accelrysdata analysis
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
ARIA1.2JP Linge, SI O'Donoghue and M Nilgesstructure solution
ARIA1.2JP Linge, SI O'Donoghue and M Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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