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- PDB-8tyu: High-resolution crystal structure of the SPX domain of XPR1 at 1.... -

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Basic information

Entry
Database: PDB / ID: 8tyu
TitleHigh-resolution crystal structure of the SPX domain of XPR1 at 1.4 angstroms
ComponentsSolute carrier family 53 member 1
KeywordsTRANSFERASE / Inositol diphosphoinositol pentakisphosphate kinase / Analog methylenebisphosphonate / PPIP5K ATP-grasp / Pyrophosphate Diphosphate
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / phosphate ion transmembrane transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / efflux transmembrane transporter activity / response to virus / virus receptor activity / plasma membrane
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: 1.4 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046 United States
CitationJournal: Cell Rep / Year: 2024
Title: Homeostatic coordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate IP8.
Authors: Li, X. / Kirkpatrick, R.B. / Wang, X. / Tucker, C.J. / Shukla, A. / Jessen, H.J. / Wang, H. / Shears, S.B. / Gu, C.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Solute carrier family 53 member 1
A: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)41,9772
Polymers41,9772
Non-polymers00
Water6,449358
1
B: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)20,9891
Polymers20,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)20,9891
Polymers20,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.290, 47.798, 71.682
Angle α, β, γ (deg.)90.00, 107.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Solute carrier family 53 member 1 / Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus ...Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus receptor X3 / X-receptor / Xenotropic and polytropic retrovirus receptor 1


Mass: 20988.633 Da / Num. of mol.: 2 / Fragment: SPX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPR1, SLC53A1, SYG1, X3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 87185 / % possible obs: 97.2 % / Redundancy: 5.3 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.024 / Rrim(I) all: 0.057 / Χ2: 0.906 / Net I/σ(I): 12.2 / Num. measured all: 465906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.3-1.323.90.6235740.8760.9660.2920.690.92380
1.32-1.354.10.61939600.8560.9610.2930.6890.9388.9
1.35-1.374.40.57541940.8970.9730.2750.640.91594.2
1.37-1.44.70.52943030.9190.9790.2510.5890.90796.6
1.4-1.4350.5343010.920.9790.2510.5890.9297.3
1.43-1.464.80.39744010.9530.9880.1950.4440.95197.9
1.46-1.550.21443510.9890.9970.1020.2380.9597.6
1.5-1.545.80.21444830.990.9970.0950.2350.93999.6
1.54-1.595.90.19644180.9880.9970.0860.2140.9199.3
1.59-1.645.80.15444380.9920.9980.0680.1680.91199.5
1.64-1.75.80.13344470.9920.9980.0590.1460.90699.6
1.7-1.765.70.10844730.9930.9980.0490.1190.90799.5
1.76-1.845.50.08244640.9960.9990.0370.0910.8999.5
1.84-1.945.30.06744320.9960.9990.0310.0740.86398.8
1.94-2.0650.05344130.9970.9990.0260.0590.87598.7
2.06-2.226.10.04744850.9970.9990.020.0510.90399.7
2.22-2.456.20.04144850.9970.9990.0180.0450.89399.9
2.45-2.86.10.03945180.9980.9990.0170.0430.89699.8
2.8-3.535.60.03744950.9970.9990.0170.0410.83999.3
3.53-505.70.04545500.990.9970.020.0490.9297.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.301 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19108 1802 2.6 %RANDOM
Rwork0.16166 ---
obs0.16243 66210 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.496 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20.02 Å2
2---0.7 Å20 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 1.4→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 0 358 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162643
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.653945
X-RAY DIFFRACTIONr_angle_other_deg0.4491.5656171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.906514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6510536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.251.7431390
X-RAY DIFFRACTIONr_mcbond_other4.2441.7421390
X-RAY DIFFRACTIONr_mcangle_it4.0762.5991734
X-RAY DIFFRACTIONr_mcangle_other4.0752.6011735
X-RAY DIFFRACTIONr_scbond_it3.3922.1611539
X-RAY DIFFRACTIONr_scbond_other3.3922.1581538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1343.0762212
X-RAY DIFFRACTIONr_long_range_B_refined5.31932.4323610
X-RAY DIFFRACTIONr_long_range_B_other5.10627.0193508
X-RAY DIFFRACTIONr_rigid_bond_restr12.23535572
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 95 -
Rwork0.212 3482 -
obs--67.45 %

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