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- PDB-7sp5: Crystal Structure of a Eukaryotic Phosphate Transporter -

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Basic information

Entry
Database: PDB / ID: 7sp5
TitleCrystal Structure of a Eukaryotic Phosphate Transporter
ComponentsPhosphate transporter
KeywordsTRANSPORT PROTEIN / Major Facilitator / Phosphate import / phosphate binding / 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 / MIRAS / Resolution: 2.9 Å
AuthorsStroud, R.M. / Pedersen, B.P. / Kumar, H. / Waight, A.B. / Risenmay, A.J. / Roe-Zurz, Z. / Chau, B.H. / Schlessinger, A. / Bonomi, M. / Harries, W. ...Stroud, R.M. / 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. / Finer-Moore, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)24485 United States
CitationJournal: 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.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2021ID: 4J05
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)118,7999
Polymers117,0772
Non-polymers1,7227
Water00
1
A: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5535
Polymers58,5391
Non-polymers1,0144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2464
Polymers58,5391
Non-polymers7083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.510, 174.510, 173.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 30 through 291 or resid 297 through 518 or resid 600 through 801))
21(chain B and (resid 30 through 159 or (resid 160...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 30 through 291 or resid 297 through 518 or resid 600 through 801))A30 - 291
121(chain A and (resid 30 through 291 or resid 297 through 518 or resid 600 through 801))A297 - 518
131(chain A and (resid 30 through 291 or resid 297 through 518 or resid 600 through 801))A600 - 801
211(chain B and (resid 30 through 159 or (resid 160...B30 - 159
221(chain B and (resid 30 through 159 or (resid 160...B160 - 161
231(chain B and (resid 30 through 159 or (resid 160...B30 - 801
241(chain B and (resid 30 through 159 or (resid 160...B30 - 801
251(chain B and (resid 30 through 159 or (resid 160...B30 - 801
261(chain B and (resid 30 through 159 or (resid 160...B346
271(chain B and (resid 30 through 159 or (resid 160...B346
281(chain B and (resid 30 through 159 or (resid 160...B30 - 801
291(chain B and (resid 30 through 159 or (resid 160...B30 - 801
2101(chain B and (resid 30 through 159 or (resid 160...B30 - 801
2111(chain B and (resid 30 through 159 or (resid 160...B30 - 801

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Components

#1: Protein Phosphate transporter


Mass: 58538.672 Da / Num. of mol.: 2
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: 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.: 5 / Source method: obtained synthetically / Formula: C15H30O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
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: 4.34 Å3/Da / Density % sol: 71.66 % / Description: hexagonal crystals 200X200x50 micrometers
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 27% (W/V) pentaerythritol propoxylate (5/4 PO/OH), 8% polyethylene glycol 400, 0.2M KCL, 0.1M sodium citrate Ph 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2012
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→75 Å / Num. obs: 42366 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.085 / Rsym value: 0.069 / Net I/σ(I): 10.23
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.01254 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 4032 / CC1/2: 0.251 / Rrim(I) all: 0.156 / Rsym value: 0.01254 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→69.27 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1982 4.86 %
Rwork0.2341 38768 -
obs0.2352 40750 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.08 Å2 / Biso mean: 96.1395 Å2 / Biso min: 42.35 Å2
Refinement stepCycle: final / Resolution: 2.9→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 115 0 6758
Biso mean--96.82 --
Num. residues----861
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2606X-RAY DIFFRACTION7.361TORSIONAL
12B2606X-RAY DIFFRACTION7.361TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.970.43671240.4132296242079
2.97-3.050.40431470.37262776292394
3.06-3.140.38011480.34242802295095
3.15-3.250.33081400.33852764290494
3.25-3.360.38291380.31642761289993
3.36-3.50.30141430.27252754289793
3.5-3.660.28741360.26282751288794
3.66-3.850.2561470.23322799294694
3.85-4.090.25481410.22462810295195
4.09-4.410.24551390.20292850298996
4.41-4.850.22161470.19492858300596
4.85-5.550.23921410.21692854299597
5.55-6.990.25581530.23182867302097
6.99-69.270.17761380.19232826296495

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