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- PDB-9b48: Asp324Glu variant of phosphate transporter PiPT from Piriformospo... -

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Basic information

Entry
Database: PDB / ID: 9b48
TitleAsp324Glu variant of phosphate transporter PiPT from Piriformospora indica
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 transporter
Similarity search - Component
Biological speciesSerendipita indica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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

Downloads & links

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Assembly

Deposited unit
B: Phosphate transporter
A: Phosphate transporter


Theoretical massNumber of molelcules
Total (without water)117,1052
Polymers117,1052
Non-polymers00
Water00
1
B: Phosphate transporter


Theoretical massNumber of molelcules
Total (without water)58,5531
Polymers58,5531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphate transporter


Theoretical massNumber of molelcules
Total (without water)58,5531
Polymers58,5531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.390, 173.390, 169.120
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_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 30 - 518 / Label seq-ID: 32 - 520

Dom-IDAuth asym-IDLabel asym-ID
d_1AB
d_2BA

NCS oper: (Code: givenMatrix: (-0.285832655569, -0.95822648567, -0.010084402327), (-0.958215845926, 0.285676489893, 0.0145373910336), (-0.0110492364615, 0.0138182951906, -0.999843472295)Vector: -71. ...NCS oper: (Code: given
Matrix: (-0.285832655569, -0.95822648567, -0.010084402327), (-0.958215845926, 0.285676489893, 0.0145373910336), (-0.0110492364615, 0.0138182951906, -0.999843472295)
Vector: -71.8872860893, -69.8757928121, 138.138498427)

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Components

#1: Protein Phosphate transporter


Mass: 58552.695 Da / Num. of mol.: 2 / Mutation: D324E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serendipita indica (fungus) / Plasmid: 83nu
Details (production host): based on p423_GAL1 with purification tags on N- and C-terminii
Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: A8N031
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, .2M KCl, .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: Oct 8, 2017
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: 4→86.7 Å / Num. obs: 16023 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.534 / Rrim(I) all: 0.561 / Net I/σ(I): 5.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4-4.110.63.1612340.1953.7999.6
4.1-4.223.25211120.2023.412
4.22-4.342.19211260.3222.301
4.34-4.471.96210830.3422.06
4.47-4.621.98310790.3472.082
4.62-4.781.7210170.4041.807
4.78-4.961.5519880.4591.631
4.96-5.161.4369370.4061.516
5.16-5.391.5139200.4851.592
5.39-5.661.5868560.5591.662
5.66-5.961.438320.5591.499
5.96-6.331.0627930.8041.115
6.33-6.760.6687430.9330.701
6.76-7.30.356740.9830.369
7.3-80.2826200.9820.298
8-8.950.1665730.9960.174
8.95-10.330.1065070.9980.111
10.33-12.650.0714220.9990.074
12.65-17.890.073210.9980.074
17.89-86.70.0391860.9990.04

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→86.69 Å / Cross valid method: FREE R-VALUE / σ(F): 3.99 / Phase error: 28.9735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2658 1595 9.96 %
Rwork0.2606 14422 -
obs0.2625 16017 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 171.26 Å2
Refinement stepCycle: LAST / Resolution: 4→86.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 0 0 6618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486782
X-RAY DIFFRACTIONf_angle_d0.75459190
X-RAY DIFFRACTIONf_chiral_restr0.03991048
X-RAY DIFFRACTIONf_plane_restr0.00441144
X-RAY DIFFRACTIONf_dihedral_angle_d12.51772312
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.275312349466 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.130.3611460.31451319X-RAY DIFFRACTION89.67
4.13-4.280.29991360.30361308X-RAY DIFFRACTION90.52
4.28-4.450.32511510.30891320X-RAY DIFFRACTION89.73
4.45-4.650.35351430.30461300X-RAY DIFFRACTION90.09
4.65-4.90.30751420.3031296X-RAY DIFFRACTION90.13
4.9-5.20.31241500.30841338X-RAY DIFFRACTION89.92
5.2-5.60.32911450.28891301X-RAY DIFFRACTION89.97
5.61-6.170.3131440.29431295X-RAY DIFFRACTION89.99
6.17-7.060.26231480.24181309X-RAY DIFFRACTION89.84
7.06-8.890.21451460.20431325X-RAY DIFFRACTION90.07
8.9-86.690.19451430.22481312X-RAY DIFFRACTION90.17

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