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- PDB-7qc0: Crystal structure of Cadmium translocating P-type ATPase -

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Basic information

Entry
Database: PDB / ID: 7qc0
TitleCrystal structure of 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
BERYLLIUM TRIFLUORIDE ION / Cadmium translocating P-type ATPase
Similarity search - Component
Biological speciesSulfitobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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)71,7453
Polymers71,6541
Non-polymers902
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-7 kcal/mol
Surface area29930 Å2
Unit cell
Length a, b, c (Å)89.028, 94.532, 128.774
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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 200 mM magnesium formate, 14 % (v/v) PEG5000, 100 mM sodium acetate, pH=4.0, and 0.5 % (v/v) 2-propanol was added as an additive.

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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: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→47.27 Å / Num. obs: 20134 / % possible obs: 97.4 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 17.8
Reflection shellResolution: 3.11→3.22 Å / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1963 / CC1/2: 0.475 / % possible all: 99.8

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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: 7QBZ

7qbz


Resolution: 3.11→47.27 Å / SU ML: 0.4857 / Cross valid method: FREE R-VALUE / Phase error: 31.7295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 1855 5.03 %
Rwork0.2447 35000 -
obs0.2459 20134 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 5 10 4710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394770
X-RAY DIFFRACTIONf_angle_d0.76666477
X-RAY DIFFRACTIONf_chiral_restr0.0477783
X-RAY DIFFRACTIONf_plane_restr0.0089839
X-RAY DIFFRACTIONf_dihedral_angle_d6.7933673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.190.39331490.45692705X-RAY DIFFRACTION97.44
3.19-3.280.41471460.37782767X-RAY DIFFRACTION99.93
3.28-3.390.28911480.33052764X-RAY DIFFRACTION99.73
3.39-3.510.28421470.2952774X-RAY DIFFRACTION99.93
3.51-3.630.34191250.3112327X-RAY DIFFRACTION98.47
3.66-3.820.44031220.43922303X-RAY DIFFRACTION85.63
3.82-4.020.3091430.2682754X-RAY DIFFRACTION100
4.02-4.270.21251460.20582774X-RAY DIFFRACTION100
4.27-4.60.20671440.18572774X-RAY DIFFRACTION100
4.6-5.060.22961450.19622756X-RAY DIFFRACTION100
5.06-5.790.27521440.22832770X-RAY DIFFRACTION100
5.79-7.290.30911480.25792773X-RAY DIFFRACTION99.73
7.3-47.270.22751480.20732759X-RAY DIFFRACTION99.42
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)
11.00025072929-0.2286701047840.2587195141140.0678589255459-0.2331089111860.639243563994-0.2697273192061.38640290895-1.15360987826-0.0405903818270.6022048903930.4237905782080.2912244026450.9558412909730.2026362311871.58199200568-0.037260571740.2764451942682.2479130256-0.04120906039050.4382114816812.113728350334.41242531813.13739117911
20.974044946498-0.02751803228950.2413682153981.8569612347-0.08342665335010.8651119411670.265738329794-0.152350753304-0.2532669937680.305567608146-0.034226156878-0.7885791191520.1080122195410.1470167672140.000242687752430.566949592863-0.01468846250860.01405077953060.524427239369-0.0351540954520.78065768480316.680920356635.555139156160.3349132718
30.665852816254-0.0767399498553-0.9870891787720.5423906597510.1401429752973.17433189882-0.1189301223011.57772157207-0.761053638861-0.129446920544-0.2202128655530.713595147492-0.301049233367-0.4736692608330.813130004622.75064173440.75848414938-0.2209777177152.60849060873-0.9131835539181.3801705702520.032793922916.09501105260.336287996374
40.89655652099-0.0805938585022-0.5604668330590.238485838519-0.04224709608051.364983925540.245384388279-0.0286160113366-0.2869030048110.044957782171-0.2055410948880.09346797704790.0402741994516-0.00623619716261-0.002731669752880.5966430263140.0279020914271-0.1402482719340.49027346151-0.04620082548550.663221604793-6.5769151804925.870616711559.4938277421
50.00614785348466-0.1148361375520.1323466695770.661868678898-0.6822707146040.6901946021210.2152168634880.361826864537-0.0113111179814-0.418512350084-0.08770642096870.0593835143402-0.02233605825110.04133389266757.62930462865E-50.9346345908440.085640823374-0.1167906285351.12440450404-0.1920112083880.6893764374230.79521255566721.369873806223.0458014293
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 138 )41 - 1381 - 98
22chain 'A' and (resid 139 through 275 )139 - 27599 - 235
33chain 'A' and (resid 276 through 326 )276 - 326236 - 286
44chain 'A' and (resid 327 through 572 )327 - 572287 - 532
55chain 'A' and (resid 573 through 678 )573 - 678533 - 638

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