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- PDB-1fd8: SOLUTION STRUCTURE OF THE CU(I) FORM OF THE YEAST METALLOCHAPERON... -

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Basic information

Entry
Database: PDB / ID: 1fd8
TitleSOLUTION STRUCTURE OF THE CU(I) FORM OF THE YEAST METALLOCHAPERONE, ATX1
ComponentsATX1 COPPER CHAPERONE
KeywordsMETAL TRANSPORT / Metallochaperone / Atx1 / HEAVY-METAL-ASSOCIATED DOMAIN / OXYGEN TOXICITY
Function / homology
Function and homology information


copper chaperone activity / copper ion transport / cellular response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / cytosol
Similarity search - Function
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 / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone ATX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, restrained energy minimization
Model type detailsminimized average
AuthorsArnesano, F. / Banci, L. / Bertini, I. / Huffman, D.L. / O'Halloran, T.V.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of the Cu(I) and apo forms of the yeast metallochaperone, Atx1.
Authors: Arnesano, F. / Banci, L. / Bertini, I. / Huffman, D.L. / O'Halloran, T.V.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / 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 / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATX1 COPPER CHAPERONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2962
Polymers8,2331
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein ATX1 COPPER CHAPERONE / ATX1


Mass: 8232.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: P38636
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D NOESY-15N HMQC
131HNHA
1412D TOCSY
15115N-1H 1J-MODULATED HSQC

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Sample preparation

DetailsContents: 1.8mM Cu(I)-Atx1 15N; 100mM phosphate buffer NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate / pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003
Bruker AVANCEBrukerAVANCE4004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRprocessing
XEASYEccles, Guentert, Billeter, Wuethrichdata analysis
DYANAGuentert, Mumenthaler, Wuethrichstructure solution
CORMABorgias, Thomas, Jamesiterative matrix relaxation
Amber6Case, Kollman et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics, restrained energy minimization
Software ordinal: 1
Details: 1184 meaningful NOEs, 42 dihedral angle restraints and 60 1JHN residual dipolar couplings
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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