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- PDB-2mzc: Metal Binding of Glutaredoxins -

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Basic information

Entry
Database: PDB / ID: 2mzc
TitleMetal Binding of Glutaredoxins
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutaredoxin / silver / dimer
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / cell redox homeostasis / cytoplasm
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SILVER ION / Glutaredoxin
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsBilinovich, S.M. / Caporoso, J.A. / Taraboletti, A. / Duangjumpa, N. / Panzner, M.J. / Prokop, J.W. / Shriver, L.P. / Leeper, T.C.
CitationJournal: To be Published
Title: Metal Binding of Glutaredoxins
Authors: Bilinovich, S.M. / Caporoso, J.A. / Taraboletti, A. / Duangjumpa, N. / Panzner, M.J. / Prokop, J.W. / Shriver, L.P. / Leeper, T.C.
History
DepositionFeb 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Glutaredoxin
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9883
Polymers19,8812
Non-polymers1081
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-11 kcal/mol
Surface area11520 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Glutaredoxin /


Mass: 9940.293 Da / Num. of mol.: 2 / Fragment: UNP residues 5-92 / Mutation: C70S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0184 / Plasmid: pAVA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YJA2
#2: Chemical ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag

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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 HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D HN(CA)CO
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.0 mM [U-99% 13C; U-99% 15N] Glutaredoxin, 0.5 mM SILVER ION, 50 mM MES, 0.01 mM TCEP, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMGlutaredoxin-1[U-99% 13C; U-99% 15N]1
0.5 mMSILVER ION-21
50 mMMES-31
0.01 mMTCEP-41
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNMRCCPNchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: FINAL REFINEMENT OF THE DOCKING OF THE MONOMER UNITS FROM CYANA OUTPUT AROUND SILVER ATOM BASED ON CHEMICAL SHIFT PERTURBATION DATA.
NMR constraintsNOE constraints total: 1299 / NOE long range total count: 356 / NOE medium range total count: 258
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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