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- PDB-8fvz: PiPT Y150A -

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Basic information

Entry
Database: PDB / ID: 8fvz
TitlePiPT Y150A
ComponentsPhosphate transporter
KeywordsTRANSPORT PROTEIN / Major facilitator / phosphate transport / membrane protein
Function / homology
Function and homology information


transmembrane transporter activity / membrane
Similarity search - Function
Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / Phosphate transporter
Similarity search - Component
Biological speciesSerendipita indica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGupta, M. / Finer-Moore, J. / Stroud, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM24485 United States
Citation
Journal: To be published
Title: Roles of PiPT residues in phosphate binding and transport tested by mutagenesis
Authors: Gupta, M. / Finer-Moore, J. / Nelson, A. / Kumar, H. / Verma, N. / Jhori, A. / Stroud, R.M.
#1: Journal: Nature / Year: 2013
Title: Crystal structure of a eukaryotic phosphate transporter.
Authors: Pedersen, B.P. / Kumar, H. / Waight, A.B. / Risenmay, A.J. / Roe-Zurz, Z. / Chau, B.H. / Schlessinger, A. / Bonomi, M. / Harries, W. / Sali, A. / Johri, A.K. / Stroud, R.M.
#2: Journal: Proc Natl Acad Sci U S A / Year: 2021
Title: Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT.
Authors: Liu, Y. / Li, C. / Gupta, M. / Verma, N. / Johri, A.K. / Stroud, R.M. / Voth, G.A.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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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)117,2725
Polymers116,8932
Non-polymers3793
Water362
1
A: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7313
Polymers58,4471
Non-polymers2842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5422
Polymers58,4471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.984, 172.984, 171.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Phosphate transporter


Mass: 58446.570 Da / Num. of mol.: 2 / Mutation: Y150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serendipita indica (fungus) / Plasmid: PRS423-GAL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: A8N031
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.3 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 27%(w/v) pentaerythritol propoxylate, 5% polyethylene glycol 400, .2M KCL, .1M sodium citrate pH5.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2021
RadiationMonochromator: Double crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 3.1→48 Å / Num. obs: 34818 / % possible obs: 100 % / Redundancy: 10.54 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.163 / Net I/σ(I): 11.59
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.1-3.184.54925780.1064.7751
3.18-3.272.93624890.2653.0841
3.27-3.362.28524400.2572.4021
3.36-3.471.61824010.4481.7031
3.47-3.581.17422830.5911.2391
3.58-3.710.84722420.7530.8911
3.71-3.850.58821630.8510.6171
3.85-40.39920570.9410.4191
4-4.180.2619600.9740.2741
4.18-4.380.18518820.9830.1951
4.38-4.620.14918260.9870.1571
4.62-4.90.1316820.9920.1371
4.9-5.240.12416210.9920.131
5.24-5.660.13614710.9920.1431
5.66-6.20.12513680.9960.1311
6.2-6.930.07912460.9980.0841
6.93-80.05810940.9980.0611
8-9.80.0469140.9990.0491
9.8-13.860.0397190.9990.0421
13.86-470.03638210.0381

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XSCALEdata scaling
XDSdata reduction
PHENIX1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.76 Å / Cross valid method: FREE R-VALUE / σ(F): 422.77 / Phase error: 43.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 3284 4.77 %random selection
Rwork0.1935 ---
obs0.2008 34690 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 23 2 6632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036792
X-RAY DIFFRACTIONf_angle_d0.5569212
X-RAY DIFFRACTIONf_dihedral_angle_d13.2382304
X-RAY DIFFRACTIONf_chiral_restr0.0391050
X-RAY DIFFRACTIONf_plane_restr0.0041149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.28821270.2872791X-RAY DIFFRACTION81
3.15-3.210.27011580.28593161X-RAY DIFFRACTION90
3.21-3.270.25541650.29533253X-RAY DIFFRACTION95
3.27-3.340.29521630.27713300X-RAY DIFFRACTION95
3.34-3.410.28521600.27163336X-RAY DIFFRACTION95
3.41-3.490.23511660.26523322X-RAY DIFFRACTION95
3.49-3.580.26651640.24553297X-RAY DIFFRACTION95
3.58-3.680.28261620.23993304X-RAY DIFFRACTION95
3.68-3.780.26331620.23583360X-RAY DIFFRACTION95
3.78-3.910.25391640.22123272X-RAY DIFFRACTION95
3.91-4.040.24381600.2263302X-RAY DIFFRACTION95
4.05-4.210.27581700.2273360X-RAY DIFFRACTION95
4.21-4.40.26881600.20473292X-RAY DIFFRACTION95
4.4-4.630.19191700.18373311X-RAY DIFFRACTION95
4.63-4.920.26831680.17753312X-RAY DIFFRACTION95
4.92-5.30.16381620.17613326X-RAY DIFFRACTION95
5.3-5.830.221700.18883316X-RAY DIFFRACTION95
5.83-6.670.17851680.19723291X-RAY DIFFRACTION95
6.68-8.40.19191640.15093317X-RAY DIFFRACTION95
8.4-47.760.17031680.17963322X-RAY DIFFRACTION95

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