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- PDB-7r0h: STRUCTURAL BASIS OF ION UPTAKE IN COPPER-TRANSPORTING P1B-TYPE ATPASES -

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Basic information

Entry
Database: PDB / ID: 7r0h
TitleSTRUCTURAL BASIS OF ION UPTAKE IN COPPER-TRANSPORTING P1B-TYPE ATPASES
ComponentsPutative copper-exporting P-type ATPase A
KeywordsMEMBRANE PROTEIN / ATPase
Function / homology
Function and homology information


ATPase-coupled monoatomic cation transmembrane transporter activity / copper ion binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / 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 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / 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 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
COPPER (II) ION / Putative copper-exporting P-type ATPase A
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsSalustros, N. / Groenberg, C. / Wang, K. / Gourdon, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of ion uptake in copper-transporting P 1B -type ATPases.
Authors: Salustros, N. / Gronberg, C. / Abeyrathna, N.S. / Lyu, P. / Oradd, F. / Wang, K. / Andersson, M. / Meloni, G. / Gourdon, P.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative copper-exporting P-type ATPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4752
Polymers70,4111
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area30950 Å2
Unit cell
Length a, b, c (Å)130.122, 151.115, 219.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

#1: Protein Putative copper-exporting P-type ATPase A


Mass: 70411.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_1059, XD48_1194 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A117KM49
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 1.5 M ammonium citrate, 0.1 M MES pH=5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.37 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 0→50 Å / Num. obs: 16266 / % possible obs: 99.63 % / Redundancy: 38 % / Biso Wilson estimate: 113.09 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1612 / Rpim(I) all: 0.02641 / Rrim(I) all: 0.1612 / Net I/σ(I): 21.49
Reflection shellResolution: 3.31→3.429 Å / Rmerge(I) obs: 1.792 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1599 / CC1/2: 0.84 / Rpim(I) all: 0.3003 / Rrim(I) all: 1.817

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFU

3rfu


Resolution: 3.31→45.93 Å / SU ML: 0.4907 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 3093 9.96 %
Rwork0.2142 27975 -
obs0.2179 16255 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.43 Å2
Refinement stepCycle: LAST / Resolution: 3.31→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 1 0 4928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01145001
X-RAY DIFFRACTIONf_angle_d1.39086782
X-RAY DIFFRACTIONf_chiral_restr0.0843827
X-RAY DIFFRACTIONf_plane_restr0.0117861
X-RAY DIFFRACTIONf_dihedral_angle_d18.854698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.360.441310.37981208X-RAY DIFFRACTION93.9
3.36-3.420.38451460.3471294X-RAY DIFFRACTION99.93
3.42-3.470.33421400.27611243X-RAY DIFFRACTION100
3.47-3.540.26411430.26511313X-RAY DIFFRACTION99.86
3.54-3.610.30031370.25191262X-RAY DIFFRACTION99.71
3.61-3.680.28831390.24251266X-RAY DIFFRACTION100
3.68-3.760.2881370.23771244X-RAY DIFFRACTION100
3.76-3.850.3071460.23811298X-RAY DIFFRACTION99.93
3.85-3.940.29671440.24581279X-RAY DIFFRACTION100
3.94-4.050.30071390.24681277X-RAY DIFFRACTION100
4.05-4.170.27241430.19661267X-RAY DIFFRACTION100
4.17-4.30.24341420.19971293X-RAY DIFFRACTION100
4.3-4.460.24031380.1751258X-RAY DIFFRACTION99.86
4.46-4.640.22341410.20161272X-RAY DIFFRACTION100
4.64-4.850.23221380.20781269X-RAY DIFFRACTION100
4.85-5.10.22021410.18761288X-RAY DIFFRACTION100
5.1-5.420.27541400.22791260X-RAY DIFFRACTION100
5.42-5.840.29521430.22911300X-RAY DIFFRACTION99.79
5.84-6.420.25661450.24921258X-RAY DIFFRACTION100
6.43-7.350.26141390.20911268X-RAY DIFFRACTION99.79
7.35-9.240.1931420.1771287X-RAY DIFFRACTION100
9.25-45.930.2071390.18491271X-RAY DIFFRACTION98.74

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