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- PDB-8b23: Time-resolved structure of K+-dependent Na+-PPase from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 8b23
TitleTime-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 600-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: 3.84 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 area6880 Å2
ΔGint-119 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.327, 111.552, 106.217
Angle α, β, γ (deg.)90.000, 109.050, 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 10 through 32 or (resid 33...
d_2ens_1(chain "B" and (resid 10 through 26 or (resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILESERA9 - 39
d_12ens_1ILEILEA41 - 56
d_13ens_1LYSALAA58 - 105
d_14ens_1ALAARGA107 - 109
d_15ens_1THRLYSA111 - 112
d_16ens_1GLYTRPA115 - 150
d_17ens_1GLYILEA152 - 159
d_18ens_1THRASNA161 - 162
d_19ens_1LEUALAA164 - 186
d_110ens_1PHEASNA188 - 213
d_111ens_1ALAVALA223 - 266
d_112ens_1HISILEA275 - 308
d_113ens_1ASPLEUA314 - 324
d_114ens_1THRTYRA326 - 340
d_115ens_1TYRTYRA342
d_116ens_1LYSLEUA344 - 346
d_117ens_1GLYSERA348 - 397
d_118ens_1THRGLYA399 - 400
d_119ens_1VALILEA402 - 467
d_120ens_1ASPGLUA474 - 476
d_121ens_1ARGLYSA478 - 479
d_122ens_1THRASPA481 - 482
d_123ens_1LEUALAA484 - 499
d_124ens_1GLYALAA501 - 507
d_125ens_1SERLEUA509 - 510
d_126ens_1ALALEUA512 - 537
d_127ens_1ALAALAA539
d_128ens_1VALLYSA541 - 569
d_129ens_1ASNARGA573 - 574
d_130ens_1ILELYSA576 - 585
d_131ens_1METGLYA587 - 588
d_132ens_1PROLEUA590 - 619
d_133ens_1GLYSERA621 - 654
d_134ens_1PROLYSA656 - 697
d_135ens_1VALPHEA699 - 702
d_21ens_1ILESERH3 - 33
d_22ens_1ILEILEH35 - 50
d_23ens_1LYSALAH52 - 99
d_24ens_1ALAARGH101 - 103
d_25ens_1THRLYSH105 - 106
d_26ens_1GLYTRPH109 - 144
d_27ens_1GLYILEH146 - 153
d_28ens_1THRASNH155 - 156
d_29ens_1LEUALAH158 - 180
d_210ens_1PHEASNH182 - 207
d_211ens_1ALALEUH217 - 305
d_212ens_1THRTYRH307 - 321
d_213ens_1TYRTYRH323
d_214ens_1LYSLEUH325 - 327
d_215ens_1GLYSERH329 - 378
d_216ens_1THRGLYH382 - 383
d_217ens_1VALGLUH385 - 453
d_218ens_1ARGLYSH455 - 456
d_219ens_1THRASPH458 - 459
d_220ens_1LEUALAH461 - 476
d_221ens_1GLYALAH478 - 484
d_222ens_1SERLEUH486 - 487
d_223ens_1ALALEUH489 - 514
d_224ens_1ALAALAH516
d_225ens_1VALLYSH518 - 546
d_226ens_1ASNARGH556 - 557
d_227ens_1ILELYSH559 - 568
d_228ens_1METGLYH570 - 571
d_229ens_1PROLEUH573 - 602
d_230ens_1GLYSERH604 - 637
d_231ens_1PROLYSH639 - 680
d_232ens_1VALPHEH682 - 685

NCS oper: (Code: givenMatrix: (0.599826139011, -0.0143116736248, -0.800002361845), (-0.00286424130667, -0.999872020832, 0.0157396975623), (-0.800125239622, -0.00714968220778, -0.599790365848)Vector: - ...NCS oper: (Code: given
Matrix: (0.599826139011, -0.0143116736248, -0.800002361845), (-0.00286424130667, -0.999872020832, 0.0157396975623), (-0.800125239622, -0.00714968220778, -0.599790365848)
Vector: -23.9447627559, 43.8744260592, -47.7646667257)

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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: 2.98 Å3/Da / Density % sol: 58.76 %
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: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.84→100.4 Å / Num. obs: 13078 / % possible obs: 90.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 210.39 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.165 / Net I/σ(I): 4.4
Reflection shellResolution: 3.84→4.17 Å / Rmerge(I) obs: 0.779 / Num. unique obs: 654 / CC1/2: 0.646

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lzq, D_1292125586

5lzq


Resolution: 3.84→100.4 Å / SU ML: 0.8303 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 58.2981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3634 663 5.08 %
Rwork0.3342 12397 -
obs0.3357 13060 73.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 249.57 Å2
Refinement stepCycle: LAST / Resolution: 3.84→100.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10029 0 13 1 10043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003410287
X-RAY DIFFRACTIONf_angle_d0.725414056
X-RAY DIFFRACTIONf_chiral_restr0.04441712
X-RAY DIFFRACTIONf_plane_restr0.00541754
X-RAY DIFFRACTIONf_dihedral_angle_d4.30761460
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.36969618145 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.84-4.130.3851310.3951433X-RAY DIFFRACTION13.22
4.13-4.550.42691220.38172046X-RAY DIFFRACTION61.75
4.55-5.210.3381510.37353142X-RAY DIFFRACTION93.13
5.21-6.560.42941740.42353385X-RAY DIFFRACTION99.97
6.56-100.40.34431850.29913391X-RAY DIFFRACTION99.22
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)
10.7363324533190.109994540102-0.3668854061250.5459568066580.39628232822-0.029598542541-0.124542115589-0.537579400635-0.676381580910.6303575476560.1974433430761.111284830061.36720005547-0.8118105814292.22403092823.55754001637-1.54041393110.865175054351.925624601021.338485609612.270788933014.538694400273.1073975082-5.30626226106
24.09412293828-2.186802675491.746403238191.37472721797-0.65527905332.4711017031-0.883611330536-2.81885705354-1.568483070051.993657708951.482707370190.9741275801420.285976997934-1.848434388362.6600450023-0.4647379013430.0802330315971.52523634030.593717579615-0.109217726482-0.04734602950798.0982483727521.4481108746-9.87948656405
31.45218037019-0.8089688547281.159514198364.254527825371.250830515615.04406521293-0.396387534965-0.971689787345-1.044195769882.736531758610.01505264382861.219321798921.73262446123-2.42241996597-4.37492422641.480987441010.2325398418790.300168081010.004903033179361.077142932610.968997296556-2.4915105206812.0497031369-16.5499578533
42.971861732840.4704124144471.251215153510.5435986539660.790103183651.306775156430.30658240809-0.9578669066610.837683919795-0.188065565480.4282175854020.664157407152-0.08070737103250.4885066248161.692973691050.9308296813920.2892915218080.06804554397440.685882737691-0.07595181526041.88526997197-7.682495743317.5492964694-17.5282977482
50.5164892670980.00372691676173-0.1549131095691.171349592891.755321891062.3873806901-0.8233490277250.245579557123-0.0436787319329-0.6109387341860.1052909225541.37443667853-0.9641358100490.457290095175-1.347682289381.121561399030.73399601606-0.1467503023770.7745785321850.1451571229551.50533898412-15.890629133535.9855717319-49.3747948389
61.14018159557-0.907346343217-0.3641788792831.06962923310.3437767908590.544265199891-1.4305640756-0.183752143908-1.48225909146-0.3950672265940.1636302323692.008341563230.691325853105-1.18280971389-6.510463143040.900324023763-0.2209436421171.09389615460.474071314962.156311275730.910629373462-14.830860228919.1385342014-43.2414957781
70.3836279826021.09174042226-0.7837252029793.05867950134-2.197856887781.451223985240.9910975367050.7539354590740.3848970440041.857466253550.6296638445781.96739295408-0.301334624297-0.3729531059227.950577089931.052396327350.1431316686290.3556523769271.77711883052-0.9988152881871.48095951664-0.57007405960631.6103568434-30.5853035621
82.933693159993.44664870738-0.4381104072198.53911463694-3.05615002991.644587747681.28845935754-1.177410299251.78372946580.639279236893-0.04995972717113.33686102936-1.53690962825-1.38032165991.404710214693.629089049731.0097544338-0.4968525171911.88306065118-0.3251488835621.84264737504-14.279425505743.6763004681-28.4929418798
93.586907292730.05394269251680.43835707153.237187634330.9051136203842.83619672942-0.34968787165-0.24634223977-0.5557350030681.59126874194-0.1827241715991.632862290620.839643819465-2.15220719503-3.00712318210.60790567668-0.1679684436140.8308832762391.27039277230.412692564997-0.399604651157-14.246974465525.8738832913-30.9479319462
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 210 )AA2 - 2101 - 209
22chain 'A' and (resid 211 through 447 )AA211 - 447210 - 444
33chain 'A' and (resid 448 through 630 )AA448 - 630445 - 606
44chain 'A' and (resid 631 through 726 )AA631 - 726607 - 702
55chain 'B' and (resid 8 through 346 )BH8 - 3461 - 326
66chain 'B' and (resid 347 through 520 )BH347 - 520327 - 494
77chain 'B' and (resid 521 through 577 )BH521 - 577495 - 551
88chain 'B' and (resid 578 through 630 )BH578 - 630552 - 589
99chain 'B' and (resid 631 through 726 )BH631 - 726590 - 685

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