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- PDB-5lzq: Crystal structure of Thermotoga maritima sodium pumping membrane ... -

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Basic information

Entry
Database: PDB / ID: 5lzq
TitleCrystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsTRANSPORT PROTEIN / Pyrophosphatase / imidodiphosphate
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 / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.495 Å
AuthorsWilkinson, C. / Kellosalo, J. / Kajander, T. / Goldman, A.
CitationJournal: Nat Commun / Year: 2016
Title: Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.
Authors: Li, K.M. / Wilkinson, C. / Kellosalo, J. / Tsai, J.Y. / Kajander, T. / Jeuken, L.J. / Sun, Y.J. / Goldman, A.
History
DepositionOct 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,43118
Polymers156,4342
Non-polymers99716
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-178 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.421, 106.763, 161.913
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 2 - 726 / Label seq-ID: 11 - 735

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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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 MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: hppA, TM_0174 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Variant (production host): BJ1991 / References: UniProt: Q9S5X0, inorganic diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / 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.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 32% PEG 400, 0.1M Tris pH 8.5, 0.1M MgCl2, 0.1M NaCl, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.49→30 Å / Num. obs: 23904 / % possible obs: 99.5 % / Redundancy: 8.8 % / Net I/σ(I): 15.83
Reflection shellResolution: 3.49→3.7 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.35 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4av3

4av3


Resolution: 3.495→29.753 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.13
RfactorNum. reflection% reflection
Rfree0.273 1194 4.99 %
Rwork0.245 --
obs0.2464 23904 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 213.38 Å2 / Biso mean: 136.0467 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.495→29.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10394 0 48 6 10448
Biso mean--159.22 134.3 -
Num. residues----1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310650
X-RAY DIFFRACTIONf_angle_d0.69814580
X-RAY DIFFRACTIONf_chiral_restr0.0251776
X-RAY DIFFRACTIONf_plane_restr0.0031827
X-RAY DIFFRACTIONf_dihedral_angle_d10.7653511
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6069X-RAY DIFFRACTION4.06TORSIONAL
12B6069X-RAY DIFFRACTION4.06TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4945-3.63420.35611280.33312434256298
3.6342-3.79930.35251310.320825062637100
3.7993-3.99920.3091300.290224722602100
3.9992-4.24910.26041320.26125202652100
4.2491-4.5760.30121320.230724942626100
4.576-5.03460.28971330.233725252658100
5.0346-5.75850.33841330.25525192652100
5.7585-7.23780.28051360.256825702706100
7.2378-29.75390.21751390.217126702809100

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