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- PDB-2lq9: Solution structure of the K60A mutant of Atox1 -

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Basic information

Entry
Database: PDB / ID: 2lq9
TitleSolution structure of the K60A mutant of Atox1
ComponentsCopper transport protein ATOX1
KeywordsMETAL BINDING PROTEIN / K60A Atox1
Function / homology
Function and homology information


metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion export / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / ATPase binding ...metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion export / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / ATPase binding / response to oxidative stress / copper ion binding / negative regulation of apoptotic process / 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 transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXi, Z. / Shi, C. / Lai, C. / Tian, C. / Liu, Y.
CitationJournal: To be Published
Title: Solution structure of the K60A mutant of Atox1
Authors: Xi, Z. / Shi, C. / Lai, C. / Tian, C. / Liu, Y.
History
DepositionFeb 28, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Copper transport protein ATOX1


Theoretical massNumber of molelcules
Total (without water)7,3551
Polymers7,3551
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7354.545 Da / Num. of mol.: 1 / Mutation: K60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00244

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCO)NH
1923D 1H-15N NOESY
11033D 1H-13C NOESY
11133D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.5 mM [U-100% 13C; U-100% 15N] entity-1, 100 mM sodium phosphate-2, 2-2.5 mM DTT-3, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.5 mM [U-100% 15N] entity-4, 100 mM sodium phosphate-5, 2-2.5 mM DTT-6, 90% H2O/10% D2O90% H2O/10% D2O
30.4-0.5 mM [U-100% 13C; U-100% 15N] entity-7, 100 mM sodium phosphate-8, 2-2.5 mM DTT-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 13C; U-100% 15N]0.4-0.51
100 mMsodium phosphate-21
mMDTT-32-2.51
mMentity-4[U-100% 15N]0.4-0.52
100 mMsodium phosphate-52
mMDTT-62-2.52
mMentity-7[U-100% 13C; U-100% 15N]0.4-0.53
100 mMsodium phosphate-83
mMDTT-92-2.53
Sample conditionsIonic strength: 0.215 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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