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- PDB-6qxa: Structure of membrane bound pyrophosphatase from Thermotoga marit... -

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Basic information

Entry
Database: PDB / ID: 6qxa
TitleStructure of membrane bound pyrophosphatase from Thermotoga maritima in complex with imidodiphosphate and N-[(2-amino-6-benzothiazolyl)methyl]-1H-indole-2-carboxamide (ATC)
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsMEMBRANE PROTEIN / membrane-bound pyrophosphatase / inhibitor
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
IMIDODIPHOSPHORIC ACID / (4S,5S)-1,2-DITHIANE-4,5-DIOL / Chem-GQB / : / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsVidilaseris, K. / Goldman, A.
Funding support Finland, United Kingdom, 6items
OrganizationGrant numberCountry
Academy of Finland308105 Finland
Academy of Finland310297 Finland
Academy of Finland265481 Finland
Academy of Finland279755 Finland
Biotechnology and Biological Sciences Research CouncilBB/M021610 United Kingdom
Jane and Aatos Erkko Foundation Finland
CitationJournal: Sci Adv / Year: 2019
Title: Asymmetry in catalysis byThermotoga maritimamembrane-bound pyrophosphatase demonstrated by a nonphosphorus allosteric inhibitor.
Authors: Vidilaseris, K. / Kiriazis, A. / Turku, A. / Khattab, A. / Johansson, N.G. / Leino, T.O. / Kiuru, P.S. / Boije Af Gennas, G. / Meri, S. / Yli-Kauhaluoma, J. / Xhaard, H. / Goldman, A.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_PDB_obs_spr / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 8, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr ...database_2 / pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: K(+)-stimulated pyrophosphate-energized sodium pump
D: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,37438
Polymers312,8694
Non-polymers2,50634
Water1448
1
A: K(+)-stimulated pyrophosphate-energized sodium pump
B: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,80420
Polymers156,4342
Non-polymers1,37018
Water181
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)157,57018
Polymers156,4342
Non-polymers1,13616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.101, 141.594, 251.980
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-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 2 through 26 or (resid 27...A2 - 267
121(chain 'A' and (resid 2 through 26 or (resid 27...A275 - 344
131(chain 'A' and (resid 2 through 26 or (resid 27...A350 - 726
141(chain 'A' and (resid 2 through 26 or (resid 27...A732
251(chain 'B' and (resid 2 through 33 or (resid 34...B2 - 267
261(chain 'B' and (resid 2 through 33 or (resid 34...B275 - 344
271(chain 'B' and (resid 2 through 33 or (resid 34...B350 - 726
281(chain 'B' and (resid 2 through 33 or (resid 34...B732
391(chain 'C' and (resid 2 through 42 or (resid 43...C2 - 267
3101(chain 'C' and (resid 2 through 42 or (resid 43...C275 - 344
3111(chain 'C' and (resid 2 through 42 or (resid 43...C350 - 726
3121(chain 'C' and (resid 2 through 42 or (resid 43...C732
4131(chain 'D' and (resid 2 through 40 or (resid 41...D2 - 267
4141(chain 'D' and (resid 2 through 40 or (resid 41...D275 - 344
4151(chain 'D' and (resid 2 through 40 or (resid 41...D350 - 726
4161(chain 'D' and (resid 2 through 40 or (resid 41...D732

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Components

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Protein , 1 types, 4 molecules ABCD

#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
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.-

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Non-polymers , 7 types, 42 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H5NO6P2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-GQB / ~{N}-[(2-azanyl-3~{H}-1,3-benzothiazol-6-yl)methyl]-1~{H}-indole-2-carboxamide


Mass: 324.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H16N4OS
#7: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.1 M NaCl, 33% polyethylene glycol (PEG) 400, and 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.424→47.48 Å / Num. obs: 48311 / % possible obs: 93.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 98.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Net I/σ(I): 9.2
Reflection shellResolution: 3.424→3.725 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1846 / CC1/2: 0.56 / Rpim(I) all: 0.52 / Rrim(I) all: 1.11 / % possible all: 57.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lzq

5lzq


Resolution: 3.41→47.48 Å / SU ML: 0.5014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9458
RfactorNum. reflection% reflection
Rfree0.2841 2000 5.5 %
Rwork0.2276 --
obs0.2307 36348 74.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 86.13 Å2
Refinement stepCycle: LAST / Resolution: 3.41→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20895 0 139 8 21042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001821461
X-RAY DIFFRACTIONf_angle_d0.451429331
X-RAY DIFFRACTIONf_chiral_restr0.03583545
X-RAY DIFFRACTIONf_plane_restr0.00243666
X-RAY DIFFRACTIONf_dihedral_angle_d2.905812319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.50.2529110.3894199X-RAY DIFFRACTION6.12
3.5-3.590.3272220.3311382X-RAY DIFFRACTION11.91
3.59-3.70.3514510.3299871X-RAY DIFFRACTION27.2
3.7-3.820.3552970.31751658X-RAY DIFFRACTION50.96
3.82-3.950.37311330.28852292X-RAY DIFFRACTION70.91
3.95-4.110.36141600.25622750X-RAY DIFFRACTION84.89
4.11-4.30.30881860.23953191X-RAY DIFFRACTION97.83
4.3-4.530.28691880.2213227X-RAY DIFFRACTION99.88
4.53-4.810.24651890.20343245X-RAY DIFFRACTION99.8
4.81-5.180.29811880.20673238X-RAY DIFFRACTION98.08
5.18-5.70.28681870.22913212X-RAY DIFFRACTION98.04
5.7-6.520.28991930.22873313X-RAY DIFFRACTION99.86
6.52-8.210.23251940.20693332X-RAY DIFFRACTION99.46
8.21-47.480.26152010.21493438X-RAY DIFFRACTION98.64

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