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- PDB-8b24: Time-resolved structure of K+-dependent Na+-PPase from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 8b24
TitleTime-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 3600-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 / : / PHOSPHATE ION / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.53 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)157,08016
Polymers156,4342
Non-polymers64614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-194 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.108, 111.068, 105.419
Angle α, β, γ (deg.)90.000, 108.900, 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 8 through 42 or (resid 43...
d_2ens_1(chain "B" and (resid 8 through 26 or (resid 27...

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_11PHEPHELEULEUAA8 - 34717 - 356
d_12GLYGLYLEULEUAA349 - 540358 - 549
d_13ALAALAALAALAAA542551
d_14VALVALLEULEUAA544 - 643553 - 652
d_15GLYGLYPHEPHEAA645 - 726654 - 735
d_16MGMGMGMGAD802
d_17MGMGMGMGAE803
d_18MGMGMGMGAF804
d_21PHEPHELEULEUBB8 - 34717 - 356
d_22GLYGLYLEULEUBB349 - 540358 - 549
d_23ALAALAALAALABB542551
d_24VALVALARGARGBB544 - 579553 - 588
d_25ASPASPLEULEUBB595 - 643604 - 652
d_26GLYGLYPHEPHEBB645 - 726654 - 735
d_27MGMGMGMGBL803
d_28MGMGMGMGBM804
d_29MGMGMGMGBN805

NCS oper: (Code: givenMatrix: (0.601688165156, -0.0292752619146, -0.79819440674), (-0.0276269152687, -0.999492909897, 0.0158327703819), (-0.798253158756, 0.0125252586825, -0.602191840223)Vector: -24. ...NCS oper: (Code: given
Matrix: (0.601688165156, -0.0292752619146, -0.79819440674), (-0.0276269152687, -0.999492909897, 0.0158327703819), (-0.798253158756, 0.0125252586825, -0.602191840223)
Vector: -24.3448916571, 44.1759806619, -47.8080156845)

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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.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
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: 2.94 Å3/Da / Density % sol: 58.2 %
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: 4.53→99.74 Å / Num. obs: 6063 / % possible obs: 87.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 287.41 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.1
Reflection shellResolution: 4.53→5.22 Å / Num. unique obs: 303 / CC1/2: 0.537
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: 5lzq, D_1292125586

5lzq


Resolution: 4.53→99.74 Å / SU ML: 0.7263 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 56.6425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3606 327 5.42 %
Rwork0.3259 5705 -
obs0.3275 6032 56.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 389.38 Å2
Refinement stepCycle: LAST / Resolution: 4.53→99.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10212 0 30 0 10242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310484
X-RAY DIFFRACTIONf_angle_d0.635614333
X-RAY DIFFRACTIONf_chiral_restr0.04281744
X-RAY DIFFRACTIONf_plane_restr0.00461792
X-RAY DIFFRACTIONf_dihedral_angle_d10.26583485
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.05076609375 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.53-5.70.5888400.4994918X-RAY DIFFRACTION18.04
5.7-99.740.35232870.31764787X-RAY DIFFRACTION93.86
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)
13.211795758451.76183901594-2.16405904393.634782841391.579576752213.39317060983-1.11357425035-2.18624148336-2.336138365591.502058576261.328198650521.489265318382.191676546581.2110772781-0.001040165179973.617633571660.2585517867110.0965426961783.403872596151.13984903554.324183078835.485956543523.0878992686-1.65156953408
21.58349244265-1.54358278051.520239802562.56648367483-3.106402096843.62307336623-0.123718001364-2.97417759066-1.326617264281.49302705603-0.107308564315-1.20504722166-0.0793659641654-0.5853492244920.08576386980262.43878295164-1.31900569551-0.01982969648884.516248055420.2965998680392.203434787837.2995603664216.688164099-9.85814351583
33.077467272070.7261026802611.953474661783.773095992941.586033009615.86549192990.936376078287-1.42062560509-2.304366273852.86667665579-1.28166222043-0.7400670045590.676547081512-1.98433672050.1268925740171.616698731950.3965758973380.4347168897032.984004785630.7695144284142.42219236301-3.8010804530316.1358474433-16.9101725234
43.22604236244-2.40768130029-4.680673348551.796519090553.37697822246.711864601431.289235632051.34147162624-0.818107240151-3.62732012155-1.929328611240.651204760913-3.44137916156-2.30556371917-0.7716051550774.174145123312.59934350473-0.2335255869473.28549748579-0.3057771331844.0627170846-23.755301050642.8175839647-47.5856502129
59.21066026189-0.3429655916491.204116388026.156220768973.825081180012.4942605891-0.3235120233430.65496369012-0.612369176519-1.157157413410.890625626521.034604182260.841250850739-0.230586875367-0.001616230115072.661772215580.677067189042-0.04269019416893.036731924311.567618393832.57338108791-11.459300745136.1146850386-45.9223560048
67.20314491441-3.646449538471.668313711963.385539617971.25089334233.335420025012.90762044156-2.76339002194-0.01988863314023.37737562789-2.652183704273.042889325262.77694835325-0.4585396269073.653429635394.0743156041-1.185198562841.62476968395.70982578535-1.381800921422.52212838593-15.43143034223.5825536304-60.2533978947
76.490138191441.059120462980.789069630496.076143429840.9397681852482.38614199774-0.1909572602371.389470202342.13406868203-0.1672319685260.1542956685371.2224339837-0.462729005413-1.01140366381-0.00215970257882.461651324061.141995231360.4485871418133.085981728520.3987778581411.90696681991-13.220887321525.7636411359-36.1004892104
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 159 )AA2 - 1591 - 158
22chain 'A' and (resid 160 through 401 )AA160 - 401159 - 400
33chain 'A' and (resid 402 through 726 )AA402 - 726401 - 710
44chain 'B' and (resid 8 through 111 )BI8 - 1111 - 104
55chain 'B' and (resid 112 through 279 )BI112 - 279105 - 272
66chain 'B' and (resid 280 through 344 )BI280 - 344273 - 337
77chain 'B' and (resid 345 through 726 )BI345 - 726338 - 705

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