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- PDB-6l85: The sodium-dependent phosphate transporter -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6l85
TitleThe sodium-dependent phosphate transporter
ComponentsPhosphate transporter
KeywordsMEMBRANE PROTEIN / PHOSPHATE BINDING / SODIUM-DEPENDENT PHOSPHATE IMPORT / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / phosphate ion transmembrane transport / membrane => GO:0016020 / membrane
Similarity search - Function
Phosphate transporter / Phosphate transporter family
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphate transporter / Phosphate transporter
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å
AuthorsTsai, J.-Y. / Sun, Y.-J.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2321-B-007-002 Taiwan
Ministry of Science and Technology (Taiwan)108-2811-B-007-504 Taiwan
CitationJournal: Sci Adv / Year: 2020
Title: Structure of the sodium-dependent phosphate transporter reveals insights into human solute carrier SLC20.
Authors: Tsai, J.-Y. / Chu, C.-H. / Lin, M.-G. / Chou, Y.-H. / Hong, R.-Y. / Yen, C.-Y. / Hsiao, C.-D. / Sun, Y.-J.
History
DepositionNov 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate transporter
B: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,47824
Polymers85,4512
Non-polymers3,02722
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-62 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.178, 112.650, 110.792
Angle α, β, γ (deg.)90.000, 119.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Phosphate transporter


Mass: 42725.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: Tmari_0259 / Plasmid: pYES2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: R4NN92, UniProt: Q9WY99*PLUS
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 176 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.86 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50mM sodium citrate (pH 5.5), 100mM NaCl, 18-20% (w/v) pentaerythritol propoxylate (5/4 PO/OH) and 10-12% polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 3, 2018
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 56236 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.052 / Χ2: 0.875 / Net I/σ(I): 12.4 / Num. measured all: 208830
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3830.35551930.8750.2270.4230.51691.2
2.38-2.483.40.30855520.9130.1910.3630.5297.6
2.48-2.593.70.22356780.9590.1330.260.54998.8
2.59-2.733.90.16256490.9810.0950.1880.59598.9
2.73-2.93.90.11156340.990.0650.1290.64798.9
2.9-3.123.90.08456720.9940.0490.0970.74599.1
3.12-3.433.90.05457120.9970.0320.0620.89799.3
3.43-3.933.90.03756970.9980.0220.0431.21699.3
3.93-4.953.80.0357070.9990.0180.0351.52199.3
4.95-303.70.02457420.9990.0140.0281.36798.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.302→29.399 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 2864 5.09 %
Rwork0.1879 53361 -
obs0.1898 56225 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.03 Å2 / Biso mean: 51.4142 Å2 / Biso min: 30.06 Å2
Refinement stepCycle: final / Resolution: 2.302→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 152 157 6300
Biso mean--64.6 61.47 -
Num. residues----801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3023-2.3420.27971140.2224234887
2.342-2.38460.2571360.223256193
2.3846-2.43040.27561440.2273266897
2.4304-2.480.24111380.216260298
2.48-2.53390.28981250.2086270899
2.5339-2.59280.23421350.2023271199
2.5928-2.65760.24091320.2031269699
2.6576-2.72940.21441500.1817267199
2.7294-2.80970.24961280.1827269099
2.8097-2.90030.20521390.1737268299
2.9003-3.00380.21781630.1931267799
3.0038-3.1240.22331440.1877269599
3.124-3.2660.25151580.1882270699
3.266-3.43790.18241390.1892270499
3.4379-3.65290.25041480.179269099
3.6529-3.93440.21321520.1785271999
3.9344-4.32920.2021750.1886269699
4.3292-4.95310.20981480.1773269599
4.9531-6.23050.26071450.207274699
6.2305-29.3990.20491510.1717269697

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