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- PDB-5ijh: Structure of the SPX domain of the human phosphate transporter XP... -

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Basic information

Entry
Database: PDB / ID: 5ijh
TitleStructure of the SPX domain of the human phosphate transporter XPR1 in complex with a sulfate ion
ComponentsXenotropic and polytropic retrovirus receptor 1
KeywordsInositol phosphate binding protein / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / Signaling protein
Function / homology
Function and homology information


: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity ...: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Science / Year: 2016
Title: Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.
Authors: Wild, R. / Gerasimaite, R. / Jung, J.Y. / Truffault, V. / Pavlovic, I. / Schmidt, A. / Saiardi, A. / Jessen, H.J. / Poirier, Y. / Hothorn, M. / Mayer, A.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xenotropic and polytropic retrovirus receptor 1
B: Xenotropic and polytropic retrovirus receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9104
Polymers50,7172
Non-polymers1922
Water77543
1
A: Xenotropic and polytropic retrovirus receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4552
Polymers25,3591
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Xenotropic and polytropic retrovirus receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4552
Polymers25,3591
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.950, 80.320, 97.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xenotropic and polytropic retrovirus receptor 1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus receptor X3 / X-receptor /


Mass: 25358.705 Da / Num. of mol.: 2 / Fragment: SPX domain, UNP Residues 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPR1, SYG1, XR / Plasmid: pMH-HC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9UBH6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.4M AmSO4, 0.1M Tris, 16% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 20166 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 65.09 Å2 / CC1/2: 1 / Rsym value: 0.067 / Net I/σ(I): 16.65
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.75 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIG

5iig


Resolution: 2.43→25.28 Å / Cor.coef. Fo:Fc: 0.9392 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 1007 5 %RANDOM
Rwork0.2014 ---
obs0.2034 20143 99.88 %-
Displacement parametersBiso mean: 91.79 Å2
Baniso -1Baniso -2Baniso -3
1--12.6918 Å20 Å20 Å2
2--21.1993 Å20 Å2
3----8.5075 Å2
Refine analyzeLuzzati coordinate error obs: 0.409 Å
Refinement stepCycle: 1 / Resolution: 2.43→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 10 43 3092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013112HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044194HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1120SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes438HARMONIC5
X-RAY DIFFRACTIONt_it3112HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion19.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3574SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.56 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2378 144 5.02 %
Rwork0.2175 2723 -
all0.2185 2867 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.896-0.17170.3653.9981-0.25512.1679-0.1162-0.1565-0.2203-0.14410.2239-0.00150.1419-0.2279-0.1077-0.1162-0.0205-0.0121-0.4161-0.0142-0.2799-8.945420.9431-22.5418
21.3894-0.04050.3053.1984-0.96632.1466-0.148-0.14470.0255-0.09550.24640.0746-0.1779-0.1111-0.0984-0.1047-0.0324-0.0349-0.3922-0.015-0.2073-3.595342.6454-16.5499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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