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- PDB-9b47: Y328F variant of P. indica phosphate transporter -

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Basic information

Entry
Database: PDB / ID: 9b47
TitleY328F variant of P. indica phosphate transporter
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
PHOSPHATE ION / Phosphate transporter
Similarity search - Component
Biological speciesSerendipita indica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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. / Johri, 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
DepositionMar 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,1403
Polymers117,0452
Non-polymers951
Water00
1
A: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6182
Polymers58,5231
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate transporter


Theoretical massNumber of molelcules
Total (without water)58,5231
Polymers58,5231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.230, 174.230, 171.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 30 through 149 or (resid 150...
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROTHRTHRAA30 - 23132 - 233
d_12ALAALAALAALAAA291293
d_13LYSLYSARGARGAA294 - 518296 - 520
d_21PROPROARGARGBB30 - 51832 - 520

NCS oper: (Code: givenMatrix: (0.974148437132, -0.225797426367, -0.00709539844448), (-0.225760239951, -0.974166361062, 0.00567582871877), (-0.00819368600014, -0.00392724082044, -0.999958719293)Vector: ...NCS oper: (Code: given
Matrix: (0.974148437132, -0.225797426367, -0.00709539844448), (-0.225760239951, -0.974166361062, 0.00567582871877), (-0.00819368600014, -0.00392724082044, -0.999958719293)
Vector: -9.07140160623, 20.7986705137, 24.9151849183)

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Components

#1: Protein Phosphate transporter


Mass: 58522.672 Da / Num. of mol.: 2 / Mutation: Y328F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serendipita indica (fungus) / Plasmid: 83nu
Details (production host): based on PRS423-GAL1, with expression tags on N- and C-termini
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.: 1 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Has protein modificationN

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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, 0.2M KCl, 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.7→113.3 Å / Num. obs: 20706 / % possible obs: 99.26 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1395 / Rpim(I) all: 0.0628 / Rrim(I) all: 0.1534 / Net I/σ(I): 8.41
Reflection shellResolution: 3.7→3.83 Å / Rmerge(I) obs: 2.45 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 2060 / CC1/2: 0.152 / CC star: 0.513 / Rpim(I) all: 1.17 / Rrim(I) all: 2.73

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→113.29 Å / Cross valid method: FREE R-VALUE / σ(F): 4.23 / Phase error: 29.4519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: least-squares refinement against twin target using NCS restraints
RfactorNum. reflection% reflection
Rfree0.2565 1986 9.65 %
Rwork0.2247 18586 -
obs0.2325 20572 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 182.66 Å2
Refinement stepCycle: LAST / Resolution: 3.7→113.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 5 0 6661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266825
X-RAY DIFFRACTIONf_angle_d0.559245
X-RAY DIFFRACTIONf_chiral_restr0.0381051
X-RAY DIFFRACTIONf_plane_restr0.00321153
X-RAY DIFFRACTIONf_dihedral_angle_d4.7897909
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.5155119485 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.790.30611240.30491140X-RAY DIFFRACTION77.39
3.79-3.890.35021490.30981349X-RAY DIFFRACTION89.93
3.89-4.010.31551470.31541355X-RAY DIFFRACTION90.03
4.01-4.130.30291430.3061341X-RAY DIFFRACTION90.36
4.14-4.280.32211380.28911328X-RAY DIFFRACTION90.52
4.28-4.450.31711450.28341357X-RAY DIFFRACTION90.35
4.46-4.660.32471440.25521321X-RAY DIFFRACTION90.17
4.66-4.90.25611380.24481345X-RAY DIFFRACTION90.69
4.9-5.210.30971410.23091343X-RAY DIFFRACTION90.5
5.21-5.610.25271380.24341326X-RAY DIFFRACTION90.57
5.61-6.180.2571430.23861352X-RAY DIFFRACTION90.43
6.18-7.070.31811410.20411340X-RAY DIFFRACTION90.48
7.07-8.90.19481470.16671350X-RAY DIFFRACTION90.18
8.91-113.290.22321430.20461344X-RAY DIFFRACTION90.32

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