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- PDB-7qbz: Crystal structure Cadmium translocating P-type ATPase -

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Basic information

Entry
Database: PDB / ID: 7qbz
TitleCrystal structure Cadmium translocating P-type ATPase
ComponentsCadmium translocating P-type ATPase
KeywordsMEMBRANE PROTEIN / P-type ATPase PIB-ATPase transporter exporter
Function / homology
Function and homology information


ATPase-coupled monoatomic cation transmembrane transporter activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / Cadmium translocating P-type ATPase
Similarity search - Component
Biological speciesSulfitobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsGroenberg, C. / Hu, Q. / Wang, K. / Gourdon, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR133-A12689 Denmark
CitationJournal: Elife / Year: 2021
Title: Structure and ion-release mechanism of P IB-4 -type ATPases.
Authors: Gronberg, C. / Hu, Q. / Mahato, D.R. / Longhin, E. / Salustros, N. / Duelli, A. / Lyu, P. / Bagenholm, V. / Eriksson, J. / Rao, K.U. / Henderson, D.I. / Meloni, G. / Andersson, M. / Croll, T. ...Authors: Gronberg, C. / Hu, Q. / Mahato, D.R. / Longhin, E. / Salustros, N. / Duelli, A. / Lyu, P. / Bagenholm, V. / Eriksson, J. / Rao, K.U. / Henderson, D.I. / Meloni, G. / Andersson, M. / Croll, T. / Godaly, G. / Wang, K. / Gourdon, P.
History
DepositionNov 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: Cadmium translocating P-type ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7823
Polymers71,6541
Non-polymers1272
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-7 kcal/mol
Surface area29920 Å2
Unit cell
Length a, b, c (Å)89.642, 93.665, 128.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Cadmium translocating P-type ATPase


Mass: 71654.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter sp. (strain NAS-14.1) (bacteria)
Strain: NAS-14.1 / Gene: NAS141_02821 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A3T2G5
#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / 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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200 mM MgCl2, 14 % (v/v) PEG1500, 10 mM tris(2-carboxyethyl)phosphine, 10 % (v/v) glycerol, 3 % 2-Methyl-2,4-pentanediol and 100 mM sodium acetate, pH=5.0.

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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 R 4M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→45.6 Å / Num. obs: 17447 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 107.68 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.5
Reflection shellResolution: 3.25→3.37 Å / Num. unique obs: 1715 / CC1/2: 0.37 / % possible all: 99.88

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UMW

4umw


Resolution: 3.25→45.57 Å / SU ML: 0.5011 / Cross valid method: FREE R-VALUE / Phase error: 30.792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 1639 5.03 %
Rwork0.2175 30960 -
obs0.2194 17447 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 6 0 4701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334771
X-RAY DIFFRACTIONf_angle_d0.81986480
X-RAY DIFFRACTIONf_chiral_restr0.0464783
X-RAY DIFFRACTIONf_plane_restr0.0075839
X-RAY DIFFRACTIONf_dihedral_angle_d5.9559673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.350.43091370.33642581X-RAY DIFFRACTION99.82
3.35-3.450.31721360.28752598X-RAY DIFFRACTION99.82
3.45-3.580.27641370.25492613X-RAY DIFFRACTION99.82
3.58-3.720.23471350.23452562X-RAY DIFFRACTION97.75
3.72-3.890.29551390.2412558X-RAY DIFFRACTION99.08
3.89-4.090.29311340.19812559X-RAY DIFFRACTION99.59
4.09-4.350.21171370.18632608X-RAY DIFFRACTION99.71
4.35-4.690.19561370.1742610X-RAY DIFFRACTION99.75
4.69-5.160.21621370.21562568X-RAY DIFFRACTION99.45
5.16-5.90.25891330.24952599X-RAY DIFFRACTION99.56
5.9-7.430.24841390.25442514X-RAY DIFFRACTION97.07
7.43-45.570.26321380.18642590X-RAY DIFFRACTION99.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2506099886930.1296524868650.0610075612597-0.141498748606-0.00426148786626-0.00857574122921-1.100065369040.674419490956-1.452556886840.7528942261320.656969690390.01080318086880.727904422219-0.4566212181260.02281767291112.04842540676-0.08700746093830.2754757144072.57640756251-0.06805164789890.52581995706611.764105110333.51853961133.44321699426
20.7974499516030.2851196099120.1173824186851.60016431930.2719795709761.318456887780.159132543588-0.194395795262-0.06750971933230.154678037695-0.097010898715-0.602511049997-0.3123456854190.03277341131871.03618533771E-50.4520779325590.05624536282020.07286739033420.4695237451520.03627300642650.78020726367916.577405284934.737697691559.8833414966
30.070850542154-0.3064189778560.1438795246510.263735261747-0.2773059423470.127537543443-0.6964514653720.2443085862020.2466165377620.264338246839-0.06912301567711.73126741296-0.353195254445-1.077181342740.00108168326342.770619181260.388379434337-0.3971183584072.18704175318-0.4354332511231.1447336051919.483912323615.5540402395-0.21048604559
41.19555264246-1.22256447472-0.8682719116630.6459068948230.25009220452.259330373670.3202867058380.0120955567546-0.4199019797630.0949428274242-0.3500703045180.0654031706249-0.0106110880729-0.0774857279678-0.02082014619590.543886443112-0.0385679116088-0.1472808154130.461925401908-0.04987812528880.714269040742-8.4508720373926.274793964961.039691835
50.676881471780.633151232749-0.5133437606860.475594718151-0.4406487208550.5932610528470.4553050911690.580654561918-0.203369871517-0.306126654061-0.3871876405210.1227119945380.4050140723410.2397893570710.1074342686460.8825731593860.506576900575-0.2789119523740.943645007024-0.3177280644730.580343272251.8549752861419.957250594627.0260300347
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 41 through 139 )41 - 1391 - 99
22chain 'A' and (resid 140 through 277 )140 - 277100 - 237
33chain 'A' and (resid 278 through 328 )278 - 328238 - 288
44chain 'A' and (resid 329 through 549 )329 - 549289 - 509
55chain 'A' and (resid 550 through 678 )550 - 678510 - 638

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