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- PDB-8b21: Time-resolved structure of K+-dependent Na+-PPase from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 8b21
TitleTime-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 0-60-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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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)159,94025
Polymers156,4342
Non-polymers3,50623
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-15 kcal/mol
Surface area42410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.022, 110.051, 107.405
Angle α, β, γ (deg.)90.000, 108.030, 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_11ALAALAGLUGLUAA4 - 21213 - 221
d_12ASNASNLEULEUAA214 - 347223 - 356
d_13GLYGLYGLYGLYAA349 - 377358 - 386
d_14TRPTRPILEILEAA379 - 399388 - 408
d_15GLYGLYLEULEUAA401 - 424410 - 433
d_16LEULEULEULEUAA426 - 540435 - 549
d_17ALAALAALAALAAA542551
d_18VALVALILEILEAA544 - 577553 - 586
d_19ARGARGGLUGLUAA579 - 583588 - 592
d_110PROPROPHEPHEAA594 - 627603 - 636
d_111LEULEULEULEUAA629 - 643638 - 652
d_112GLYGLYLEULEUAA645 - 671654 - 680
d_113GLYGLYLYSLYSAA673 - 721682 - 730
d_114VALVALPHEPHEAA723 - 726732 - 735
d_21ALAALAGLUGLUBB4 - 21213 - 221
d_22ASNASNLEULEUBB214 - 347223 - 356
d_23GLYGLYGLYGLYBB349 - 377358 - 386
d_24TRPTRPILEILEBB379 - 399388 - 408
d_25GLYGLYLEULEUBB401 - 424410 - 433
d_26LEULEULEULEUBB426 - 540435 - 549
d_27ALAALAALAALABB542551
d_28VALVALILEILEBB544 - 577553 - 586
d_29ARGARGPHEPHEBB579 - 627588 - 636
d_210LEULEULEULEUBB629 - 643638 - 652
d_211GLYGLYLEULEUBB645 - 671654 - 680
d_212GLYGLYLYSLYSBB673 - 721682 - 730
d_213VALVALPHEPHEBB723 - 726732 - 735

NCS oper: (Code: givenMatrix: (0.592123174476, -0.0284940725171, -0.805343550344), (-0.0303723864086, -0.999453708303, 0.0130308519647), (-0.80527489989, 0.0167443360713, -0.592665135483)Vector: -24. ...NCS oper: (Code: given
Matrix: (0.592123174476, -0.0284940725171, -0.805343550344), (-0.0303723864086, -0.999453708303, 0.0130308519647), (-0.80527489989, 0.0167443360713, -0.592665135483)
Vector: -24.0502912841, 43.7690584191, -49.339885969)

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 4 types, 23 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.25 %
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: 0.9768 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: 0.9768 Å / Relative weight: 1
ReflectionResolution: 2.57→102.13 Å / Num. obs: 37297 / % possible obs: 93.8 % / Redundancy: 48.1 % / Biso Wilson estimate: 70.28 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2
Reflection shellResolution: 2.57→2.89 Å / Num. unique obs: 1868 / CC1/2: 0.519
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: 4AV3

4av3


Resolution: 2.59→102.13 Å / SU ML: 0.2746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 1757 4.72 %
Rwork0.2195 35433 -
obs0.2203 37190 64.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.3 Å2
Refinement stepCycle: LAST / Resolution: 2.59→102.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10425 0 212 1 10638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310923
X-RAY DIFFRACTIONf_angle_d0.563514813
X-RAY DIFFRACTIONf_chiral_restr0.03811767
X-RAY DIFFRACTIONf_plane_restr0.00391832
X-RAY DIFFRACTIONf_dihedral_angle_d13.08033750
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.42674510268 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.660.412640.3347102X-RAY DIFFRACTION2.43
2.66-2.740.4776180.3463347X-RAY DIFFRACTION8.35
2.74-2.830.3715250.3307670X-RAY DIFFRACTION15.62
2.83-2.930.3567600.30871037X-RAY DIFFRACTION24.94
2.93-3.050.3023880.29811811X-RAY DIFFRACTION42.9
3.05-3.190.28391210.29452755X-RAY DIFFRACTION64.96
3.19-3.350.29791770.28063398X-RAY DIFFRACTION80.14
3.35-3.560.28472110.24584038X-RAY DIFFRACTION96.2
3.56-3.840.21771870.21364269X-RAY DIFFRACTION99.71
3.84-4.230.21072160.18894212X-RAY DIFFRACTION99.91
4.23-4.840.20892080.16864231X-RAY DIFFRACTION99.82
4.84-6.090.23242020.22384282X-RAY DIFFRACTION99.98
6.09-102.130.22692400.22584281X-RAY DIFFRACTION99.3
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)
10.3162121209050.320070171109-0.0156392125810.376943052716-0.02246508759160.191451637308-0.00327453529787-0.508328435231-0.5427110413420.377712456058-0.0527744861589-0.1873873456080.0473039190093-0.01582544613430.2835018682270.6315490805280.1441204870390.1728631201020.6772049186180.4087256183670.4565325930816.121418183153.07149704571-2.32590674905
20.3905761153310.07474771463170.09511269085130.513785273403-0.1054667873810.751294512724-0.148526298083-0.515755832435-0.1013299491610.3764924279770.01706427480040.0326681540217-0.1972504720210.269222450794-0.03718714624730.3556286110310.01568690531510.04980118325630.3957268567970.05707765809910.3370239806076.0252736392318.8196987935-10.6991304825
30.8097285534710.403449027263-0.2553133879550.213570918897-0.02936423633640.6185979630330.0148400158062-0.5599774650250.02136831495010.592517728982-0.1865523354850.409629860205-0.174510165232-0.399143288277-0.2685109407560.5565696696970.1214916973780.2719466087520.7065726733370.05106056551210.383726832975-3.2531241253717.2329355632-3.32650784382
40.6168090186460.06850271751340.1325324239370.4831279491830.01751328702630.54826116836-0.149146819021-0.220303700602-0.2648110673910.3584308278680.1084646706240.2547750358070.0284090075526-0.007218866740450.05830489545690.1992050876940.05852999986080.2443604838590.1948728785350.06373245039590.344254041605-6.9760237666811.4683025029-20.9069919125
50.0342226605606-0.00791479098598-0.03252089922120.1128659173150.04477947867360.120890693437-0.003840438404410.1996788498260.0920650068931-0.0925206354853-0.07343837804680.195826939624-0.318309041059-0.186034906699-1.015530200250.4938266346710.0939141781135-0.2469245185840.7503577296980.8187167722971.01731889079-23.300922744341.8772296198-50.4815422884
60.172390886575-0.1425036845790.07725032655740.6522807004310.1838069369210.337774456936-0.06611872283840.5959055533930.356330155598-0.240096211410.04329001011610.345734069286-0.207624242199-0.269566119784-0.3094191155650.364344681071-0.0474860578015-0.09573910878880.781319189510.2637514893770.489033549241-12.502335213432.2606826348-51.4949206189
70.508257449064-0.1341428004470.1571686067630.583169809013-0.3040669473170.318353816654-0.1341552812370.4624432647780.225911278475-0.1249949418710.1119516811810.3967786434010.0801276156255-0.16961741534-0.03559400924640.226854263893-0.07652153089640.007411436815290.4111671542210.096643302350.504143813123-13.353792856723.226487439-40.3544249397
80.0820724417021-0.08008968753050.1057649008670.231194162460.2317470504340.741145743597-0.03067809553930.1616873934390.486304079742-0.001424938842630.08564072049190.428063942532-0.295842143136-0.278010932221-0.06154755025950.3013153685690.01059303746910.0109691713170.300698042090.1133588609660.612894909916-15.01290730531.2865461973-31.5137740677
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 447 )AA168 - 447167 - 446
33chain 'A' and (resid 448 through 521 )AA448 - 521447 - 520
44chain 'A' and (resid 522 through 726 )AA522 - 726521 - 716
55chain 'B' and (resid 4 through 112 )BL4 - 1121 - 109
66chain 'B' and (resid 113 through 343 )BL113 - 343110 - 340
77chain 'B' and (resid 344 through 582 )BL344 - 582341 - 579
88chain 'B' and (resid 583 through 726 )BL583 - 726580 - 713

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