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- PDB-8b22: Time-resolved structure of K+-dependent Na+-PPase from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 8b22
TitleTime-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 300-seconds post reaction initiation with Na+
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsMEMBRANE PROTEIN / Membrane bound pyrophosphatase / enzyme / complex
Function / homology
Function and homology information


Na+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / sodium ion transmembrane transporter activity / inorganic diphosphate phosphatase activity / potassium ion binding / sodium ion transmembrane transport / calcium ion binding / magnesium ion binding / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase
Similarity search - Domain/homology
DIPHOSPHATE / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 Å
AuthorsStrauss, J. / Vidilaseris, K. / Goldman, A.
Funding supportEuropean Union, United Kingdom, Finland, 3items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission722687European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021610/1 United Kingdom
Academy of Finland1322609 and 308105 Finland
Citation
Journal: Embo Rep. / Year: 2024
Title: Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases.
Authors: Strauss, J. / Wilkinson, C. / Vidilaseris, K. / de Castro Ribeiro, O.M. / Liu, J. / Hillier, J. / Wichert, M. / Malinen, A.M. / Gehl, B. / Jeuken, L.J. / Pearson, A.R. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K(+)-stimulated pyrophosphate-energized sodium pump
B: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7057
Polymers156,4342
Non-polymers2715
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-116 kcal/mol
Surface area42180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.928, 110.626, 106.154
Angle α, β, γ (deg.)90.000, 108.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 26 or (resid 27...
d_2ens_1(chain "B" and (resid 4 through 42 or (resid 43...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAPROPROAA4 - 21613 - 225
d_12ASPASPLEULEUAA218 - 347227 - 356
d_13GLYGLYLEULEUAA349 - 540358 - 549
d_14ALAALAALAALAAA542551
d_15VALVALILEILEAA544 - 577553 - 586
d_16ARGARGGLUGLUAA579 - 583588 - 592
d_17PROPROPHEPHEAA594 - 627603 - 636
d_18LEULEULEULEUAA629 - 643638 - 652
d_19GLYGLYLEULEUAA645 - 671654 - 680
d_110GLYGLYHISHISAA673 - 681682 - 690
d_111ALAALALYSLYSAA683 - 721692 - 730
d_112VALVALPHEPHEAA723 - 726732 - 735
d_21ALAALAPROPROBB4 - 21613 - 225
d_22ASPASPLEULEUBB218 - 347227 - 356
d_23GLYGLYLEULEUBB349 - 540358 - 549
d_24ALAALAALAALABB542551
d_25VALVALILEILEBB544 - 577553 - 586
d_26ARGARGPHEPHEBB579 - 627588 - 636
d_27LEULEULEULEUBB629 - 643638 - 652
d_28GLYGLYLEULEUBB645 - 671654 - 680
d_29GLYGLYHISHISBB673 - 681682 - 690
d_210ALAALALYSLYSBB683 - 721692 - 730
d_211VALVALPHEPHEBB723 - 726732 - 735

NCS oper: (Code: givenMatrix: (0.58899328382, -0.0242247484807, -0.807774766365), (-0.019355639933, -0.999686752524, 0.0158668217286), (-0.807906102723, 0.00628954609096, -0.589277668669)Vector: -23. ...NCS oper: (Code: given
Matrix: (0.58899328382, -0.0242247484807, -0.807774766365), (-0.019355639933, -0.999686752524, 0.0158668217286), (-0.807906102723, 0.00628954609096, -0.589277668669)
Vector: -23.977452766, 46.2246768244, -48.4721093303)

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Components

#1: Protein K(+)-stimulated pyrophosphate-energized sodium pump / Membrane-bound sodium-translocating pyrophosphatase / Pyrophosphate-energized inorganic ...Membrane-bound sodium-translocating pyrophosphatase / Pyrophosphate-energized inorganic pyrophosphatase / Na(+)-PPase / Tm-PPase


Mass: 78217.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: hppA, TM_0174 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9S5X0, EC: 7.2.3.-
#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 60 mM Tris-HCl pH 8.0, 26% v/v PEG400, 175 mM KCl, 2.4 mM MgCl2, 2 mM K4PPi, 20 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.97→100.81 Å / Num. obs: 14163 / % possible obs: 95.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 88.03 Å2 / CC1/2: 0.975 / Net I/σ(I): 6.1
Reflection shellResolution: 3.97→4.09 Å / Num. unique obs: 708 / CC1/2: 0.837
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292125586

Resolution: 3.98→79.7 Å / SU ML: 0.4661 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 1400 9.92 %
Rwork0.2326 12719 -
obs0.2357 14119 88.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.51 Å2
Refinement stepCycle: LAST / Resolution: 3.98→79.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10431 0 13 1 10445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210748
X-RAY DIFFRACTIONf_angle_d0.590314667
X-RAY DIFFRACTIONf_chiral_restr0.03961767
X-RAY DIFFRACTIONf_plane_restr0.00431833
X-RAY DIFFRACTIONf_dihedral_angle_d10.24143650
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.556376190805 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.98-4.120.2823840.2832795X-RAY DIFFRACTION55.74
4.12-4.280.2351080.2465953X-RAY DIFFRACTION66.65
4.28-4.480.2631180.20571122X-RAY DIFFRACTION77.6
4.48-4.710.20061390.20441263X-RAY DIFFRACTION88.57
4.71-5.010.22711600.21071377X-RAY DIFFRACTION95.7
5.01-5.40.28911620.22491416X-RAY DIFFRACTION99.81
5.4-5.940.3061490.25751469X-RAY DIFFRACTION99.94
5.94-6.790.27341560.2391429X-RAY DIFFRACTION99.94
6.8-8.560.22971650.2151451X-RAY DIFFRACTION99.75
8.56-79.70.29971590.24711444X-RAY DIFFRACTION97.09
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)
12.13852850095-0.225249019643-1.225307447530.1421246646260.5152304603951.21191423354-0.520496736459-0.768058956898-1.06720698480.7567487089750.02095296601660.1056421928920.711382414062-0.068277737879-0.3832894752721.656929061020.1384910215110.4398838915211.178147597570.3854429989970.9801475911655.944396350693.88114806293-2.25762807558
23.323143372161.563971414131.548715908332.66435625102-0.5201572244551.014913589-0.0840390159166-1.04920916495-0.1065296978480.9239292631860.2686857130920.647598525162-0.0572348204637-0.3051046685820.0697156070920.8153552434920.1315304148280.2821287796970.6882206111810.1649254559280.457232227980.056439031023316.9693290738-13.1898875561
30.1432516561910.4313419994070.1564973411892.054575478671.396143020032.09746082951-0.388154067717-0.2647582303230.11735861841-0.383924934884-0.5337060359122.38221648744-1.24897788281-1.474964413190.4575340026750.9710769311380.265125256064-0.7946701508551.17353241081.433821027572.33553501507-23.405794887743.540158818-49.5133046724
42.61487350189-1.02914609664-0.1904895782811.561354936410.8663473178510.382658049592-0.2018580894771.903115368820.5893414467-0.59955332690.09323935698741.059976236490.058830749348-0.401616533683-0.1353988873130.751305866116-0.0728595203413-0.2145268011281.225757469970.2712086683711.00220915549-12.614101408233.8814607775-50.7872976687
51.16824129991-0.394904954430.8627199937050.8332807595920.02399341670790.577708069835-0.8477934228450.697435264968-0.972284792138-0.665869451920.3854205203460.856748632148-0.259272820735-0.493665610229-0.08395526005791.00676351706-0.1828600777060.1319100699650.7988196658370.06339801123171.12942959419-11.421283569316.4575825141-42.9939805428
60.7774430339060.05916223560670.425176099840.6027572687650.130096335880.932505908757-0.3827292311690.611581367836-0.44536709076-0.005530384720790.5110617814720.789891105114-0.0403614593284-1.09564748878-0.02733750966760.376752561987-0.0951548196534-0.3655886079791.246942780940.2490794181861.89699112415-24.574364193528.2880698921-43.723429532
70.04547887802990.276378613702-0.009226360587161.2528941086-0.02977755095331.10547279286-0.0173717013248-0.2218803868582.55879075130.3087541260130.4728830457750.0864600035036-0.5068173489720.163992368732-0.09002024199510.809906963501-0.1017623963290.09576811539750.8768193316620.08048945626981.38642284082-4.6831531509634.6868947929-29.8483681736
80.1471820866070.006218004326650.4209460767411.198463407420.9937588605011.65512119475-0.3849072790440.778235644530.4519716641290.4744944288610.3100186115330.61551711710.0834863524571-0.670469463652-0.04506303614960.627230625383-0.01012531320530.03396617708270.5840837363270.1195171346460.66416552758-15.063075144432.5097368644-30.8359267411
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 167 )AA2 - 1671 - 166
22chain 'A' and (resid 168 through 726 )AA168 - 726167 - 716
33chain 'B' and (resid 4 through 112 )BC4 - 1121 - 109
44chain 'B' and (resid 113 through 343 )BC113 - 343110 - 340
55chain 'B' and (resid 344 through 448 )BC344 - 448341 - 445
66chain 'B' and (resid 449 through 521 )BC449 - 521446 - 518
77chain 'B' and (resid 522 through 582 )BC522 - 582519 - 579
88chain 'B' and (resid 583 through 726 )BC583 - 726580 - 713

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