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- PDB-7r0g: STRUCTURAL BASIS OF ION UPTAKE IN COPPER-TRANSPORTING P1B-TYPE ATPASES -

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Basic information

Entry
Database: PDB / ID: 7r0g
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
Putative copper-exporting P-type ATPase A
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 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
B: Putative copper-exporting P-type ATPase A


Theoretical massNumber of molelcules
Total (without water)140,8222
Polymers140,8222
Non-polymers00
Water0
1
A: Putative copper-exporting P-type ATPase A


Theoretical massNumber of molelcules
Total (without water)70,4111
Polymers70,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative copper-exporting P-type ATPase A


Theoretical massNumber of molelcules
Total (without water)70,4111
Polymers70,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.194, 226.056, 111.106
Angle α, β, γ (deg.)90.000, 134.062, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -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.: 2
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

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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: 4.11 Å3/Da / Density % sol: 70.05 %
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 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 36001 / % possible obs: 93.94 % / Redundancy: 8.4 % / Biso Wilson estimate: 191.11 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2057 / Rpim(I) all: 0.07477 / Rrim(I) all: 0.219 / Net I/σ(I): 6.88
Reflection shellResolution: 4.011→4.154 Å / Rmerge(I) obs: 3.855 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 1863 / CC1/2: 0.996 / CC star: 0.503 / Rpim(I) all: 1.386 / Rrim(I) all: 4.099

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFU

3rfu


Resolution: 4.01→48.75 Å / SU ML: 0.777 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3117 1788 9.99 %
Rwork0.2625 16115 -
obs0.2673 17903 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 196.93 Å2
Refinement stepCycle: LAST / Resolution: 4.01→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9841 0 0 0 9841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00529989
X-RAY DIFFRACTIONf_angle_d1.06313547
X-RAY DIFFRACTIONf_chiral_restr0.05831654
X-RAY DIFFRACTIONf_plane_restr0.00891718
X-RAY DIFFRACTIONf_dihedral_angle_d5.53441394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.01-4.120.4651110.41871009X-RAY DIFFRACTION75.78
4.12-4.240.37561370.37891243X-RAY DIFFRACTION95.5
4.24-4.380.36071420.35711281X-RAY DIFFRACTION97.33
4.38-4.530.37661420.34341278X-RAY DIFFRACTION97.33
4.53-4.710.34351410.33511275X-RAY DIFFRACTION96.92
4.71-4.930.33541420.32711269X-RAY DIFFRACTION97.18
4.93-5.190.34891410.32121271X-RAY DIFFRACTION96.51
5.19-5.510.34881390.31911253X-RAY DIFFRACTION95.54
5.51-5.940.29931400.31621259X-RAY DIFFRACTION95.11
5.94-6.530.34681370.30641231X-RAY DIFFRACTION93.63
6.54-7.470.27451220.27951100X-RAY DIFFRACTION83.81
7.48-9.410.2671480.2091327X-RAY DIFFRACTION99.26
9.41-48.750.29211460.18641319X-RAY DIFFRACTION98.52

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