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- PDB-9qz0: MINPP1 from Bacteroides thetaiotaomicron E325N mutant complex wit... -

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Basic information

Entry
Database: PDB / ID: 9qz0
TitleMINPP1 from Bacteroides thetaiotaomicron E325N mutant complex with myo-inositol hexakisphosphate
Componentsmultiple inositol polyphosphate histidine 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 / INOSITOL HEXAKISPHOSPHATE / Multiple inositol polyphosphate phosphatase 1
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLi, A.W.H. / Shang, X.Y. / 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
AA: multiple inositol polyphosphate histidine phosphatase 1
BA: multiple inositol polyphosphate histidine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3575
Polymers98,3772
Non-polymers1,9803
Water11,836657
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-29 kcal/mol
Surface area33800 Å2
Unit cell
Length a, b, c (Å)52.833, 120.410, 75.939
Angle α, β, γ (deg.)90.000, 108.040, 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 histidine phosphatase 1 / MINPP


Mass: 49188.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: VPI-5482 / Gene: BT_4744 / Variant: E325N / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89YI8
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Crystal growth 0.2 M ammonium acetate pH 5.0 18 % (w/v) PEG 3350 Crystal soak 5mM myo-Ins(1,2,3,4,5,6) hexaphosphate 0.2 M ammonium acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.86→26.4 Å / Num. obs: 73771 / % possible obs: 97.29 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.62 Å2 / CC1/2: 0.993 / Net I/σ(I): 10.33
Reflection shellResolution: 1.86→1.93 Å / Mean I/σ(I) obs: 2.81 / Num. unique obs: 7312 / CC1/2: 0.298

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→26.4 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 3704 5.03 %
Rwork0.1652 69878 -
obs0.1666 73582 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.05 Å2
Refinement stepCycle: LAST / Resolution: 1.86→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6423 0 108 657 7188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766813
X-RAY DIFFRACTIONf_angle_d0.94059279
X-RAY DIFFRACTIONf_chiral_restr0.0591990
X-RAY DIFFRACTIONf_plane_restr0.00751158
X-RAY DIFFRACTIONf_dihedral_angle_d6.0189913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.2711530.25492675X-RAY DIFFRACTION96.06
1.88-1.910.27521400.24442614X-RAY DIFFRACTION95.92
1.91-1.940.29661160.24332670X-RAY DIFFRACTION96.3
1.94-1.970.2711530.23542624X-RAY DIFFRACTION96.16
1.97-20.24871410.22162670X-RAY DIFFRACTION96.43
2-2.030.24161450.20182664X-RAY DIFFRACTION97.2
2.03-2.060.23391290.19922672X-RAY DIFFRACTION96.65
2.06-2.10.2331370.1892664X-RAY DIFFRACTION96.35
2.1-2.140.19861440.17512656X-RAY DIFFRACTION96.89
2.14-2.190.20451240.17212684X-RAY DIFFRACTION96.46
2.19-2.230.21251370.16422659X-RAY DIFFRACTION96.41
2.23-2.290.19041240.16852670X-RAY DIFFRACTION95.72
2.29-2.340.20691420.15952627X-RAY DIFFRACTION96.92
2.34-2.410.19781410.16312671X-RAY DIFFRACTION96.67
2.41-2.480.22311430.15682696X-RAY DIFFRACTION98.27
2.48-2.560.19131570.15892722X-RAY DIFFRACTION98.66
2.56-2.650.22321280.1592734X-RAY DIFFRACTION98.25
2.65-2.750.1911470.15772667X-RAY DIFFRACTION97.67
2.75-2.880.20561470.15972723X-RAY DIFFRACTION98.32
2.88-3.030.18941580.16282699X-RAY DIFFRACTION98.08
3.03-3.220.17311350.16032727X-RAY DIFFRACTION98.72
3.22-3.470.17391470.15562750X-RAY DIFFRACTION98.6
3.47-3.820.19721530.14972714X-RAY DIFFRACTION98.66
3.82-4.370.18141490.14032744X-RAY DIFFRACTION98.57
4.37-5.490.13391550.13982738X-RAY DIFFRACTION98.54
5.5-26.40.16381590.16442744X-RAY DIFFRACTION98.04
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)
10.8660645739860.1308584242530.05810232521511.09773145367-0.4064002821851.124190278870.0379169930994-0.0717671442998-0.07773467095270.0316134117454-0.009192099006410.08460486747170.0263325703325-0.0375160949927-0.01122513483170.08750307427910.01105380211570.002115365513760.103618583932-0.007031361394470.09476224492124.86906740197-0.762706585636.545836668
21.13151492467-0.2080566231680.04908692978920.7598434175760.1206971931981.13139863147-0.023979730340.1249608732640.0825606515463-0.00437352815923-0.006752047286620.0342765199795-0.1353508699160.07051548155110.02517946994170.136179415912-0.0422735573376-0.009838665235320.104650443060.01569465495280.10509639099714.167404747419.167493607167.6523865109
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 22 through 423)AAA22 - 4231 - 393
22(chain 'B' and resid 21 through 423)BAB21 - 4231 - 394

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