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

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Basic information

Entry
Database: PDB / ID: 5lzr
TitleCrystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with tungstate and magnesium
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsTRANSPORT PROTEIN / Pyrophosphatase / Tungstate
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
TUNGSTATE(VI)ION / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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 / 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 / _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_seq_id / _struct_conn.ptnr2_label_asym_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)157,0278
Polymers156,4342
Non-polymers5936
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-112 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.720, 108.870, 105.810
Angle α, β, γ (deg.)90.000, 108.790, 90.000
Int Tables number4
Space group name H-MP1211
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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 19% PEG 350 monomethylether, 0.1M MES-NaOH pH 6.5, 0.2M CaCl2, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.214 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 29597 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.3
Reflection shellRedundancy: 3.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.65 / % possible all: 92.8

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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: 4→28.462 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.03
RfactorNum. reflection% reflection
Rfree0.2785 2934 9.91 %
Rwork0.2323 --
obs0.2369 29597 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.69 Å2 / Biso mean: 134.8663 Å2 / Biso min: 97.95 Å2
Refinement stepCycle: final / Resolution: 4→28.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9782 0 14 0 9796
Biso mean--182.37 --
Num. residues----1387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049996
X-RAY DIFFRACTIONf_angle_d1.19413655
X-RAY DIFFRACTIONf_chiral_restr0.0411668
X-RAY DIFFRACTIONf_plane_restr0.0061711
X-RAY DIFFRACTIONf_dihedral_angle_d12.9843240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5408X-RAY DIFFRACTION10.509TORSIONAL
12B5408X-RAY DIFFRACTION10.509TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0001-4.06550.31441220.31189131196
4.0655-4.13540.32571470.273812571404100
4.1354-4.21040.26811560.253212921448100
4.2104-4.29110.31951220.262112991421100
4.2911-4.37840.27631360.251212671403100
4.3784-4.47320.31591520.253312651417100
4.4732-4.57690.29661480.250313041452100
4.5769-4.69090.2781340.230912391373100
4.6909-4.81710.28041430.242212701413100
4.8171-4.95810.34661530.236113071460100
4.9581-5.11730.27051360.255912591395100
5.1173-5.2990.29461400.25212951435100
5.299-5.50970.34011340.263712621396100
5.5097-5.75850.31351370.268312731410100
5.7585-6.05940.3391300.270413161446100
6.0594-6.43490.33051400.274512791419100
6.4349-6.92510.29821350.245512891424100
6.9251-7.60990.25151510.218912701421100
7.6099-8.68360.20951290.163812511380100
8.6836-10.83910.17851480.16421254140299
10.8391-28.46290.32811410.24771226136796

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