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- PDB-2mmz: Solution structure of the apo form of human glutaredoxin 5 -

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Basic information

Entry
Database: PDB / ID: 2mmz
TitleSolution structure of the apo form of human glutaredoxin 5
ComponentsGlutaredoxin-related protein 5, mitochondrial
KeywordsMETAL BINDING PROTEIN / monothiol glutaredoxins / iron-sulfur protein biogenesis / [2Fe-2S] cluster protein
Function / homology
Function and homology information


protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis ...protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / mitochondrial matrix / neuronal cell body / dendrite / mitochondrion / metal ion binding
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-related protein 5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsBanci, L. / Brancaccio, D. / Ciofi-Baffoni, S. / Del Conte, R. / Gadepalli, R. / Mikolajczyk, M. / Neri, S. / Piccioli, M. / Winkelmann, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: [2Fe-2S] cluster transfer in iron-sulfur protein biogenesis.
Authors: Banci, L. / Brancaccio, D. / Ciofi-Baffoni, S. / Del Conte, R. / Gadepalli, R. / Mikolajczyk, M. / Neri, S. / Piccioli, M. / Winkelmann, J.
History
DepositionMar 25, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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-related protein 5, mitochondrial


Theoretical massNumber of molelcules
Total (without water)13,1711
Polymers13,1711
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 / 80target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Glutaredoxin-related protein 5, mitochondrial / Monothiol glutaredoxin-5


Mass: 13170.894 Da / Num. of mol.: 1 / Fragment: unp residues 35-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRX5, C14orf87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q86SX6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D (H)CCH-TOCSY
1412D 1H-1H NOESY
1523D CBCA(CO)NH
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HBHA(CO)NH
11023D HN(CO)CA
11113D 1H-15N NOESY
11223D 1H-13C NOESY aliphatic
11323D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] apo glutaredoxin 5, 50 mM potassium phosphate, 5 mM DTT, 5 mM GSH, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] apo glutaredoxin 5, 50 mM potassium phosphate, 5 mM DTT, 5 mM GSH, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMapo glutaredoxin 5-1[U-100% 15N]0.5-11
50 mMpotassium phosphate-21
5 mMDTT-31
5 mMGSH-41
mMapo glutaredoxin 5-5[U-100% 13C; U-100% 15N]0.5-12
50 mMpotassium phosphate-62
5 mMDTT-72
5 mMGSH-82
Sample conditionsIonic strength: 50 mM potassium phosphate / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
CARA2Keller and Wuthrichchemical shift assignment
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichautomatic noes assignment
TALOSCornilescu, Delaglio and Baxbackbone torsion angle calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.data analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
PSVSBhattacharya and Montelionestructure validation
CINGVuister, Sousa da Silva, and Doreleijersstructure validation
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1999 / NOE intraresidue total count: 555 / NOE long range total count: 456 / NOE medium range total count: 439 / NOE sequential total count: 549 / Hydrogen bond constraints total count: 38 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 94 / Protein psi angle constraints total count: 92
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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