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- PDB-5ijj: Structure of the SPX domain of Chaetomium thermophilum Glyceropho... -

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Basic information

Entry
Database: PDB / ID: 5ijj
TitleStructure of the SPX domain of Chaetomium thermophilum Glycerophosphodiester Phosphodiesterase 1 in complex with inositol hexakisphosphate (InsP6)
ComponentsSPX domain
Keywordsinositol polyphosphate binding protein / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / Hydrolase
Function / homology
Function and homology information


glycerophosphocholine phosphodiesterase activity / glycerophospholipid catabolic process
Similarity search - Function
: / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / SPX domain / SPX domain / SPX domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...: / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / SPX domain / SPX domain / SPX domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
ACETATE ION / INOSITOL HEXAKISPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: SPX domain
B: SPX domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,86010
Polymers44,5732
Non-polymers2,2878
Water1,51384
1
A: SPX domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1305
Polymers22,2861
Non-polymers8434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPX domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7315
Polymers22,2861
Non-polymers1,4444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.363, 53.366, 94.314
Angle α, β, γ (deg.)90.00, 113.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SPX domain


Mass: 22286.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0005190 / Plasmid: pMH-HC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: G0RY29, glycerophosphodiester phosphodiesterase
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3350, 0.1M ammonium acetate, 0.1M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 28959 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rsym value: 0.06 / Net I/σ(I): 20.5
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.28 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIG

5iig


Resolution: 1.95→19.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.211 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25089 1448 5 %RANDOM
Rwork0.20173 ---
obs0.20421 27510 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.756 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å2-0 Å20.8 Å2
2---1.6 Å2-0 Å2
3----2 Å2
Refinement stepCycle: 1 / Resolution: 1.95→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 128 84 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022853
X-RAY DIFFRACTIONr_bond_other_d0.0020.022730
X-RAY DIFFRACTIONr_angle_refined_deg2.2292.023873
X-RAY DIFFRACTIONr_angle_other_deg1.09636286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54823.969131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44815512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0041523
X-RAY DIFFRACTIONr_chiral_restr0.1330.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02622
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_it1.5112.4221329
X-RAY DIFFRACTIONr_mcbond_other1.512.4211328
X-RAY DIFFRACTIONr_mcangle_it2.1953.6161657
X-RAY DIFFRACTIONr_mcangle_other2.1953.6181658
X-RAY DIFFRACTIONr_scbond_it3.1693.351524
X-RAY DIFFRACTIONr_scbond_other3.1683.3491524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7354.9822216
X-RAY DIFFRACTIONr_long_range_B_refined9.19526.34912285
X-RAY DIFFRACTIONr_long_range_B_other9.1926.31612261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 69 -
Rwork0.371 1313 -
obs--62.99 %
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)
13.90282.8791-1.80865.9078-4.4875.79780.3152-0.6631-0.02810.5673-0.5378-0.3881-0.70420.69420.22260.113-0.062-0.04520.2218-0.03830.0595-26.0757-0.663334.1523
20.61791.1585-2.15073.1701-4.6337.93880.10670.04940.08480.0660.07610.1242-0.3064-0.0989-0.18290.16640.0032-0.01570.12440.01010.1534-26.386212.10579.4927
30.530.5145-2.04910.8237-2.59769.19940.0591-0.16520.01770.25-0.4673-0.2292-0.73641.06590.40820.2328-0.1008-0.1290.43590.16790.2258-13.732113.69781.9794
43.55211.1876-1.26875.8431-3.28198.1903-0.0778-0.2723-0.1889-0.1861-0.114-0.21120.2110.26040.19180.01370.0248-0.00120.0678-0.01240.0334-27.3817-7.333425.9628
59.18.117-10.12228.3276-7.564214.5001-0.2045-0.011-0.2922-0.1609-0.0768-0.44320.25990.70250.28130.25810.06-0.07130.50890.0850.1671-15.18425.6741.1195
62.1877-0.04353.27456.9399-6.183711.69780.02030.2672-0.4163-0.438-0.4239-1.24070.5091.4770.40360.22070.11180.10110.4277-0.02350.3423-14.162630.702510.5102
72.93462.5084-4.2122.2679-4.07667.9449-0.10820.0523-0.0354-0.15480.0337-0.02910.3121-0.04360.07440.16870.02560.02970.0428-0.02310.1622-32.922716.534627.6149
83.33191.7607-3.78464.3883-3.30246.6938-0.1398-0.1887-0.4138-0.0895-0.4455-0.56340.37410.62630.58530.0590.0272-0.03820.24010.07570.1885-33.944310.282249.1029
95.33371.8947-3.6494.5367-3.50677.32390.0169-0.2855-0.14870.1771-0.1802-0.1494-0.2280.56250.16330.0322-0.0004-0.00620.0803-0.0230.0513-25.384331.608223.1159
100.2090.3199-1.3916.9971-6.365914.84280.05-0.16850.02810.3465-0.1613-0.2627-0.49530.19590.11130.0259-0.0383-0.00550.4073-0.01880.2569-34.330117.935649.8793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 55
2X-RAY DIFFRACTION2A56 - 79
3X-RAY DIFFRACTION3A80 - 114
4X-RAY DIFFRACTION4A115 - 156
5X-RAY DIFFRACTION5A157 - 175
6X-RAY DIFFRACTION6B21 - 44
7X-RAY DIFFRACTION7B45 - 79
8X-RAY DIFFRACTION8B80 - 113
9X-RAY DIFFRACTION9B114 - 158
10X-RAY DIFFRACTION10B159 - 177

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