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- PDB-2kkh: Structure of the zinc binding domain of the ATPase HMA4 -

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Basic information

Entry
Database: PDB / ID: 2kkh
TitleStructure of the zinc binding domain of the ATPase HMA4
ComponentsPutative heavy metal transporter
KeywordsMETAL TRANSPORT / Zinc transport / metal binding / metal selectivity / Arabidopsis thaliana / ferredoxin fold / ATP-binding / Hydrolase / Nucleotide-binding / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


cadmium ion transport / : / Cd2+-exporting ATPase / P-type Zn2+ transporter / P-type zinc transporter activity / zinc ion transmembrane transporter activity / zinc ion transport / cadmium ion transmembrane transporter activity / metal ion transport / plasmodesma ...cadmium ion transport / : / Cd2+-exporting ATPase / P-type Zn2+ transporter / P-type zinc transporter activity / zinc ion transmembrane transporter activity / zinc ion transport / cadmium ion transmembrane transporter activity / metal ion transport / plasmodesma / response to cobalt ion / ATPase-coupled monoatomic cation transmembrane transporter activity / response to metal ion / response to zinc ion / response to cadmium ion / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase ...P-type ATPase, subfamily IB / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative cadmium/zinc-transporting ATPase HMA4 / Putative heavy metal transporter
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsZimmerman, M. / Clarke, O. / Gulbis, J.M. / Keizer, D.W. / Jarvis, R.S. / Cobbett, C.S. / Hinds, M.G. / Xiao, Z. / Wedd, A.G.
CitationJournal: Biochemistry / Year: 2009
Title: Metal binding affinities of Arabidopsis zinc and copper transporters: selectivities match the relative, but not the absolute, affinities of their amino-terminal domains
Authors: Zimmermann, M. / Clarke, O. / Gulbis, J.M. / Keizer, D.W. / Jarvis, R.S. / Cobbett, C.S. / Hinds, M.G. / Xiao, Z. / Wedd, A.G.
History
DepositionJun 20, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative heavy metal transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8122
Polymers10,7461
Non-polymers651
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative heavy metal transporter


Mass: 10746.498 Da / Num. of mol.: 1 / Fragment: UNP residues 2-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q8RVG7, UniProt: O64474*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the N-terminal zinc binding domain of the P1B-type ATPase HMA4 from Arabidopsis thaliana
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D HN(CO)CA
1613D 1H-13C NOESY
1713D 1H-15N NOESY
1813D C(CO)NH
NMR detailsText: Heteronuclear spectra were recorded on spectrometers equipped with cryogenically cooled probes.

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] protein-1, 50 mM potassium phosphate-2, 0.02 % sodium azide-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-21
0.02 %sodium azide-31
Sample conditionsIonic strength: 50 / pH: 7.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker AGcollection
TopSpin2Bruker AGprocessing
XEASY3.13Bartels et al.chemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH22Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1683 / NOE intraresidue total count: 811 / NOE long range total count: 377 / NOE medium range total count: 212 / NOE sequential total count: 283 / Hydrogen bond constraints total count: 30 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 58
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.016 Å / Distance rms dev error: 0.001 Å

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