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- PDB-9b49: K459Q variant of P. indica phosphate transporter -

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Basic information

Entry
Database: PDB / ID: 9b49
TitleK459Q 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: 3.1 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. / 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
A: Phosphate transporter
B: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4918
Polymers117,0752
Non-polymers1,4166
Water00
1
A: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2454
Polymers58,5381
Non-polymers7083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2454
Polymers58,5381
Non-polymers7083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.670, 173.670, 172.070
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 99 or resid 104...
d_2ens_1(chain "B" and (resid 30 through 149 or resid 151...

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_11PROPROPHEPHEAA30 - 9932 - 101
d_12VALVALASPASPAA104 - 149106 - 151
d_13PROPROTHRTHRAA151 - 231153 - 233
d_14LYSLYSARGARGAA294 - 518296 - 520
d_15PO4PO4PO4PO4AC601
d_16BNGBNGBNGBNGAD602
d_17BNGBNGBNGBNGAE603
d_21PROPROASPASPBB30 - 14932 - 151
d_22PROPROTHRTHRBB151 - 231153 - 233
d_23LYSLYSARGARGBB294 - 518296 - 520
d_24PO4PO4PO4PO4BF601
d_25BNGBNGBNGBNGBG602
d_26BNGBNGBNGBNGBH603

NCS oper: (Code: givenMatrix: (-0.272157313823, 0.962174392326, 0.0122815017066), (0.962252752537, 0.272132596789, 0.00367287349574), (0.000191747871954, 0.0128175082071, -0.999917833982)Vector: -72. ...NCS oper: (Code: given
Matrix: (-0.272157313823, 0.962174392326, 0.0122815017066), (0.962252752537, 0.272132596789, 0.00367287349574), (0.000191747871954, 0.0128175082071, -0.999917833982)
Vector: -72.5347247899, 69.1799702514, 83.3055715025)

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Components

#1: Protein Phosphate transporter


Mass: 58537.617 Da / Num. of mol.: 2 / Mutation: K459Q
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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
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,.2M KCl, .1M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2019
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: 3.1→48 Å / Num. obs: 35004 / % possible obs: 95.9 % / Redundancy: 2.9 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1305 / Rpim(I) all: 0.0917 / Rrim(I) all: 0.1604 / Net I/σ(I): 6.21
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 2.64 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 3528 / CC1/2: 0.0895 / CC star: 0.405 / Rpim(I) all: 1.86 / Rrim(I) all: 3.2 / % possible all: 67.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.86 Å / Cross valid method: FREE R-VALUE / σ(F): 2.26 / Phase error: 43.8949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: refined against a least-squares twin target using NCS restraints
RfactorNum. reflection% reflection
Rfree0.2404 1714 5.09 %
Rwork0.2155 31946 -
obs0.2377 33660 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 94 0 6666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256839
X-RAY DIFFRACTIONf_angle_d0.59719276
X-RAY DIFFRACTIONf_chiral_restr0.03751071
X-RAY DIFFRACTIONf_plane_restr0.00411143
X-RAY DIFFRACTIONf_dihedral_angle_d5.692933
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.31407262478 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.190.2711910.30021753X-RAY DIFFRACTION60.28
3.19-3.290.30851340.29112543X-RAY DIFFRACTION86.32
3.29-3.410.34511420.2942747X-RAY DIFFRACTION94.37
3.41-3.550.27431460.29412775X-RAY DIFFRACTION94.94
3.55-3.710.3781480.30232794X-RAY DIFFRACTION94.84
3.71-3.910.32921440.30622743X-RAY DIFFRACTION94.39
3.91-4.150.27921480.28962776X-RAY DIFFRACTION94.91
4.15-4.470.27821490.27312778X-RAY DIFFRACTION94.81
4.47-4.920.2811460.2412755X-RAY DIFFRACTION94.51
4.92-5.630.28241420.22772757X-RAY DIFFRACTION94.39
5.63-7.080.21981450.20442781X-RAY DIFFRACTION94.95
7.09-47.860.21391400.17222783X-RAY DIFFRACTION94.53

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