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- PDB-9g8j: Structure of K+-dependent Na+-PPase from Thermotoga maritima in c... -

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Basic information

Entry
Database: PDB / ID: 9g8j
TitleStructure of K+-dependent Na+-PPase from Thermotoga maritima in complex with zoledronate
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsMEMBRANE PROTEIN / Inhibitor / complex / enzyme / transporter
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
ZOLEDRONIC ACID / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsVidilaseris, K. / Liu, J. / Goldman, A.
Funding support Finland, United Kingdom, 5items
OrganizationGrant numberCountry
Academy of Finland308105 Finland
Academy of Finland1355187 Finland
Academy of Finland1322609 Finland
Academy of Finland13364501 Finland
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T006048/1 United Kingdom
CitationJournal: Elife / Year: 2024
Title: Conformational dynamics and asymmetry in multimodal inhibition of membrane-bound pyrophosphatases
Authors: Liu, J. / Shah, A. / Ma, Y. / Hardman, K. / Johansson, N.G. / Ribeiro, O. / Brookfield, A. / Bowen, A. / Yli-Kauhaluoma, J. / Xhaard, H. / Jeuken, L.J. / Goldman, A. / Pliotas, C. / Vidilaseris, K.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)314,85625
Polymers312,8694
Non-polymers1,98821
Water18010
1
A: K(+)-stimulated pyrophosphate-energized sodium pump
B: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,17312
Polymers156,4342
Non-polymers73910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: K(+)-stimulated pyrophosphate-energized sodium pump
D: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,68413
Polymers156,4342
Non-polymers1,24911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.185, 147.362, 252.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 21 or (resid 22...
d_2ens_1(chain "B" and (resid 2 through 21 or (resid 22...
d_3ens_1(chain "C" and (resid 2 through 21 or (resid 22...
d_4ens_1(chain "D" and (resid 2 through 25 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_11TYRTYRVALVALAA2 - 2511 - 34
d_12ARGARGGLUGLUAA27 - 3036 - 39
d_13LYSLYSALAALAAA36 - 10945 - 118
d_14THRTHRVALVALAA111 - 267120 - 276
d_15VALVALVALVALAA275 - 310284 - 319
d_16SERSERSERSERAA314323
d_17PROPROGLNGLNAA317 - 348326 - 357
d_18LEULEULEULEUAA350 - 353359 - 362
d_19PHEPHEPROPROAA355 - 478364 - 487
d_110VALVALLYSLYSAA480 - 591489 - 600
d_111TYRTYRPHEPHEAA596 - 726605 - 735
d_112ZOLZOLZOLZOLAE801
d_21TYRTYRVALVALBB2 - 2511 - 34
d_22ARGARGGLUGLUBB27 - 3036 - 39
d_23LYSLYSALAALABB36 - 10945 - 118
d_24THRTHRVALVALBB111 - 310120 - 319
d_25SERSERSERSERBB314323
d_26PROPROGLNGLNBB317 - 348326 - 357
d_27LEULEULEULEUBB350 - 353359 - 362
d_28PHEPHEPROPROBB355 - 478364 - 487
d_29VALVALLYSLYSBB480 - 591489 - 600
d_210TYRTYRPHEPHEBB596 - 726605 - 735
d_211ZOLZOLZOLZOLBJ801
d_31TYRTYRGLUGLUCC2 - 3011 - 39
d_32LYSLYSVALVALCC36 - 26745 - 276
d_33VALVALVALVALCC275 - 310284 - 319
d_34SERSERGLNGLNCC314 - 348323 - 357
d_35LEULEUPROPROCC350 - 478359 - 487
d_36VALVALLYSLYSCC480 - 591489 - 600
d_37TYRTYRPHEPHECC596 - 726605 - 735
d_38ZOLZOLZOLZOLCO801
d_41TYRTYRVALVALDD2 - 2511 - 34
d_42ARGARGGLUGLUDD27 - 3036 - 39
d_43LYSLYSALAALADD36 - 10945 - 118
d_44THRTHRVALVALDD111 - 267120 - 276
d_45VALVALSERSERDD275 - 314284 - 323
d_46PROPROLEULEUDD317 - 353326 - 362
d_47PHEPHEPHEPHEDD355 - 726364 - 735
d_48ZOLZOLZOLZOLDT801

NCS oper:
IDCodeMatrixVector
1given(-0.765345800449, -0.434797018402, 0.474549637576), (-0.436686939908, -0.190843174606, -0.879137872703), (0.472811085158, -0.880074107956, -0.0438091572184)-81.5770662894, 3.18144153989, 43.2796044466
2given(0.999180967454, -0.0395434406696, 0.00858548640412), (0.0403740698443, 0.988439013485, -0.146144623935), (-0.00270716844582, 0.146371557759, 0.989225979399)-0.401930405573, -61.0529861496, -17.2446204427
3given(-0.745800656901, -0.430822026779, 0.508108021398), (-0.531193985218, -0.075689117247, -0.843862611803), (0.402012848346, -0.899257215024, -0.172401075961)-81.5799569376, -67.2075673053, 26.27650113

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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.: 4
Source method: isolated from a genetically manipulated source
Details: His6-tag protein arrangement / Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: hppA, TM_0174 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9S5X0, EC: 7.2.3.-
#2: Chemical
ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID


Mass: 272.090 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Comment: medication*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 0.1 M NaCl, 33 % PEG400, and 4 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.257→127.255 Å / Num. obs: 33220 / % possible obs: 93.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 118.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.039 / Rrim(I) all: 0.143 / Net I/σ(I): 10.2
Reflection shellResolution: 3.26→3.31 Å / Rmerge(I) obs: 1.785 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1661 / CC1/2: 0.573 / Rpim(I) all: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→48.22 Å / SU ML: 0.5357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.3861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3062 1669 5.05 %
Rwork0.2655 31373 -
obs0.2676 33042 55.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.65 Å2
Refinement stepCycle: LAST / Resolution: 3.26→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20730 0 115 10 20855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004121264
X-RAY DIFFRACTIONf_angle_d0.656629066
X-RAY DIFFRACTIONf_chiral_restr0.04933538
X-RAY DIFFRACTIONf_plane_restr0.00353627
X-RAY DIFFRACTIONf_dihedral_angle_d11.89437053
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.877666538139
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.864858392171
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.929775280764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.26-3.350.386170.3705119X-RAY DIFFRACTION2.58
3.35-3.460.4281110.356314X-RAY DIFFRACTION6.71
3.46-3.580.3962350.3456560X-RAY DIFFRACTION12.04
3.58-3.730.3623490.3446859X-RAY DIFFRACTION18.43
3.73-3.90.3325620.31171228X-RAY DIFFRACTION26.11
3.9-4.10.3079930.29071966X-RAY DIFFRACTION41.93
4.1-4.360.33671590.25643115X-RAY DIFFRACTION65.72
4.36-4.70.2951920.23744065X-RAY DIFFRACTION85.98
4.7-5.170.29982690.25554608X-RAY DIFFRACTION98.05
5.17-5.910.32472490.29064779X-RAY DIFFRACTION99.72
5.92-7.450.33632530.29264808X-RAY DIFFRACTION99.98
7.45-48.220.28632900.2524952X-RAY DIFFRACTION99.36

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