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- PDB-9qyx: MINPP1 from Bacteroides thetaiotaomicron T30E mutant complex with... -

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Basic information

Entry
Database: PDB / ID: 9qyx
TitleMINPP1 from Bacteroides thetaiotaomicron T30E mutant complex with myo-inositol hexakissulfate
ComponentsMultiple inositol polyphosphate phosphatase 1
KeywordsHYDROLASE / Histidine phosphatase / phytase / mutant / complex
Function / homologymultiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / hydrolase activity / membrane / D-MYO-INOSITOL-HEXASULPHATE / Multiple inositol polyphosphate phosphatase 1
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsShang, X.Y. / Salmon, M. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: To Be Published
Title: A Structural Basis for the Stereospecificity of Multiple Inositol Polyphosphate Phosphatases
Authors: Salmon, M. / Shang, X.Y. / Li, A.W.H. / Hemmings, A.M.
History
DepositionApr 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple inositol polyphosphate phosphatase 1
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1056
Polymers98,4632
Non-polymers2,6424
Water11,818656
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5533
Polymers49,2311
Non-polymers1,3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5533
Polymers49,2311
Non-polymers1,3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.930, 118.580, 75.080
Angle α, β, γ (deg.)90.000, 107.410, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Multiple inositol polyphosphate phosphatase 1 / 2 / 3-bisphosphoglycerate 3-phosphatase


Mass: 49231.438 Da / Num. of mol.: 2 / Mutation: T30E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: VPI-5482 / Gene: BT_4744 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q89YI8, multiple inositol-polyphosphate phosphatase, 2,3-bisphosphoglycerate 3-phosphatase
#2: Chemical
ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M ammonium acetate pH 5.0 18 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.54→50.51 Å / Num. obs: 127568 / % possible obs: 97.97 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.41 Å2 / CC1/2: 1 / Net I/σ(I): 15.95
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 10978 / CC1/2: 0.53 / % possible all: 84.31

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→50.51 Å / SU ML: 0.1889 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.199 6324 4.96 %
Rwork0.1785 121237 -
obs0.1795 127561 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.63 Å2
Refinement stepCycle: LAST / Resolution: 1.54→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 144 656 7311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01026979
X-RAY DIFFRACTIONf_angle_d1.55329528
X-RAY DIFFRACTIONf_chiral_restr0.36311054
X-RAY DIFFRACTIONf_plane_restr0.00841168
X-RAY DIFFRACTIONf_dihedral_angle_d14.83841012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.3751900.34023247X-RAY DIFFRACTION78.42
1.56-1.580.33661880.31973468X-RAY DIFFRACTION85.44
1.58-1.60.33341890.30413694X-RAY DIFFRACTION89.18
1.6-1.620.2892110.26543857X-RAY DIFFRACTION94.6
1.62-1.640.27982060.25613989X-RAY DIFFRACTION97.58
1.64-1.660.25992240.24474018X-RAY DIFFRACTION97.34
1.66-1.680.26952140.23294045X-RAY DIFFRACTION99.42
1.68-1.710.25412070.22784198X-RAY DIFFRACTION99.71
1.71-1.730.27682150.24284086X-RAY DIFFRACTION99.86
1.73-1.760.2692020.25234106X-RAY DIFFRACTION99.79
1.76-1.790.2672050.2384096X-RAY DIFFRACTION99.88
1.79-1.830.23752000.22974187X-RAY DIFFRACTION99.93
1.83-1.860.26142030.21064075X-RAY DIFFRACTION99.95
1.86-1.90.20622180.194127X-RAY DIFFRACTION99.82
1.9-1.940.2252260.18814087X-RAY DIFFRACTION99.88
1.94-1.990.22192210.19134079X-RAY DIFFRACTION99.86
1.99-2.040.20152010.19034175X-RAY DIFFRACTION99.84
2.04-2.090.22791920.1864102X-RAY DIFFRACTION99.91
2.09-2.150.20182040.18794121X-RAY DIFFRACTION99.65
2.15-2.220.20762030.18064152X-RAY DIFFRACTION99.91
2.22-2.30.22862330.18474115X-RAY DIFFRACTION99.93
2.3-2.390.21422390.18164066X-RAY DIFFRACTION99.91
2.39-2.50.19622250.18364132X-RAY DIFFRACTION99.98
2.5-2.630.21371940.18474127X-RAY DIFFRACTION100
2.63-2.80.20742220.18464139X-RAY DIFFRACTION99.86
2.8-3.010.19952260.18094098X-RAY DIFFRACTION99.98
3.01-3.320.17912150.17214165X-RAY DIFFRACTION99.93
3.32-3.80.19162160.16114136X-RAY DIFFRACTION100
3.8-4.780.15372420.13264132X-RAY DIFFRACTION99.95
4.78-50.510.15411930.1574218X-RAY DIFFRACTION99.82
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)
10.5406919992580.138087950752-0.1577270383340.802016395522-0.2594649745530.7839659929440.0244273236843-0.0624471861333-0.04898161182260.0605911789252-0.00990071880470.04943022460450.008501066208880.0194906559874-0.01580439538550.1581203514470.00376016851485-0.01001904992390.18934290220.00591949965510.16121049103316.7528210303-8.648009431390.120642414192
20.777589786559-0.123900590548-0.05596294061490.689215177808-0.05214746892571.095259420940.03561934207690.09736954377070.0581296058374-0.0190605587489-0.02506800129530.042842114181-0.123992072665-0.111476299943-0.008122368985070.161667694839-0.0059778974478-0.01076692953940.1969565325750.01505799724640.13603941958627.286820384110.614250358830.4680631279
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 18 through 424)AA18 - 4241 - 400
22(chain 'B' and resid 20 through 424)BB20 - 4241 - 398

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