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- PDB-2kt3: Structure of Hg-NmerA, Hg(II) complex of the N-terminal domain of... -

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Basic information

Entry
Database: PDB / ID: 2kt3
TitleStructure of Hg-NmerA, Hg(II) complex of the N-terminal domain of Tn501 Mercuric Reductase
ComponentsMercuric reductase
KeywordsOXIDOREDUCTASE / NmerA / MerA / mercuric reductase / HMA domain / Mercuric resistance / Mercury / Metal-binding
Function / homology
Function and homology information


mercury(II) reductase / mercury (II) reductase (NADP+) activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / detoxification of mercury ion / mercury ion binding / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Mercury(II) reductase / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. ...Mercury(II) reductase / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Alpha-Beta Plaits - #100 / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Mercuric reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMiller, S.M. / Ledwidge, R. / Danacea, F. / Dotsch, V.
Citation
Journal: Biochemistry / Year: 2010
Title: NmerA of Tn501 mercuric ion reductase: structural modulation of the pKa values of the metal binding cysteine thiols.
Authors: Ledwidge, R. / Hong, B. / Dotsch, V. / Miller, S.M.
#1: Journal: Biochemistry / Year: 2005
Title: NmerA, the metal binding domain of mercuric ion reductase, removes Hg2+ from proteins, delivers it to the catalytic core, and protects cells under glutathione-depleted conditions
Authors: Ledwidge, R. / Patel, B. / Dong, A. / Fiedler, D. / Falkowski, M. / Zelikova, J. / Summers, A.O. / Pai, E.F. / Miller, S.M.
History
DepositionJan 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 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: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1202
Polymers6,9191
Non-polymers2011
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 Mercuric reductase / Hg(II) reductase


Mass: 6919.002 Da / Num. of mol.: 1 / Fragment: N-terminal HMA domain, residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: merA / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P00392, mercury(II) reductase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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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 1H-15N TOCSY
1313D 1H-15N NOESY
1433D 1H-13C NOESY
1523D HNCA
1623D CBCA(CO)NH
1723D C(CO)NH
1823D HBHA(CO)NH
1923D H(CCO)NH
11013D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-2.0 mM [U-100% 15N] NmerA polypeptide-1, stoichiometric with NmerA mM MERCURY (II) ION-2, 10 mM [U-100% 2H] HEPES-3, 90% H2O/10% D2O90% H2O/10% D2O
21.0-2.0 mM [U-100% 13C; U-100% 15N] NmerA polypeptide-4, stoichiometric with NmerA mM MERCURY (II) ION-5, 10 mM [U-100% 2H] HEPES-6, 90% H2O/10% D2O90% H2O/10% D2O
31.0-2.0 mM [U-100% 13C; U-100% 15N] NmerA polypeptide-7, stoichiometric with NmerA mM MERCURY (II) ION-8, 10 mM [U-100% 2H] HEPES-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMNmerA polypeptide-1[U-100% 15N]1.0-2.01
mMMERCURY (II) ION-21
10 mMHEPES-3[U-100% 2H]1
mMNmerA polypeptide-4[U-100% 13C; U-100% 15N]1.0-2.02
mMMERCURY (II) ION-52
10 mMHEPES-6[U-100% 2H]2
mMNmerA polypeptide-7[U-100% 13C; U-100% 15N]1.0-2.03
mMMERCURY (II) ION-83
10 mMHEPES-9[U-100% 2H]3
Sample conditionsIonic strength: 0.0176 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospinprocessing
XwinNMRBruker Biospincollection
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
DYANAGuntert, Braun and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readenergy minimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thostructure analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 689 / NOE intraresidue total count: 133 / NOE long range total count: 225 / NOE medium range total count: 170 / NOE sequential total count: 161
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.027 Å / Distance rms dev error: 0.006 Å

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