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- PDB-9qz2: MINPP1 from Bacteroides thetaiotaomicron A324D/E325N mutant -

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Basic information

Entry
Database: PDB / ID: 9qz2
TitleMINPP1 from Bacteroides thetaiotaomicron A324D/E325N mutant
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 / PHOSPHATE ION / Multiple inositol polyphosphate phosphatase 1
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
A: Multiple inositol polyphosphate phosphatase 1
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8134
Polymers98,6232
Non-polymers1902
Water5,368298
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4062
Polymers49,3111
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4062
Polymers49,3111
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.470, 117.910, 76.110
Angle α, β, γ (deg.)90.000, 108.130, 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: 49311.395 Da / Num. of mol.: 2 / Mutation: A324D,E325N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4744 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q89YI8, multiple inositol-polyphosphate phosphatase, 2,3-bisphosphoglycerate 3-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
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: I24 / Wavelength: 0.969 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.95→26.61 Å / Num. obs: 62382 / % possible obs: 97.96 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.13
Reflection shellResolution: 1.95→2.024 Å / Mean I/σ(I) obs: 2.21 / Num. unique obs: 6296 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→26.61 Å / SU ML: 0.193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 3156 5.06 %
Rwork0.1873 59159 -
obs0.1889 62315 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 10 298 6788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766663
X-RAY DIFFRACTIONf_angle_d0.93439022
X-RAY DIFFRACTIONf_chiral_restr0.0553961
X-RAY DIFFRACTIONf_plane_restr0.00911146
X-RAY DIFFRACTIONf_dihedral_angle_d7.1937876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.32031380.29612562X-RAY DIFFRACTION98.68
1.98-2.010.34711280.28172640X-RAY DIFFRACTION99.43
2.01-2.050.31111490.26992575X-RAY DIFFRACTION99.49
2.05-2.080.30641280.25362602X-RAY DIFFRACTION99.78
2.08-2.120.29431200.23972621X-RAY DIFFRACTION99.38
2.12-2.160.26481370.23152621X-RAY DIFFRACTION99.49
2.16-2.20.261430.23372582X-RAY DIFFRACTION99.6
2.2-2.250.29481350.20922598X-RAY DIFFRACTION99.31
2.25-2.310.2461500.20752610X-RAY DIFFRACTION99.21
2.31-2.360.21861440.19142588X-RAY DIFFRACTION98.95
2.36-2.430.26951450.19672576X-RAY DIFFRACTION98.84
2.43-2.50.24341270.19742601X-RAY DIFFRACTION98.41
2.5-2.580.22851500.19562539X-RAY DIFFRACTION98.53
2.58-2.670.24081540.19312584X-RAY DIFFRACTION98.52
2.67-2.780.20981340.1892565X-RAY DIFFRACTION97.16
2.78-2.90.24041300.19442540X-RAY DIFFRACTION97.52
2.9-3.060.24391390.1942537X-RAY DIFFRACTION96.47
3.06-3.250.2231240.19432515X-RAY DIFFRACTION95.31
3.25-3.50.21621340.18372507X-RAY DIFFRACTION94.52
3.5-3.850.2051280.16862506X-RAY DIFFRACTION96.1
3.85-4.40.18981430.1592584X-RAY DIFFRACTION97.88
4.4-5.540.16021380.15432612X-RAY DIFFRACTION98.81
5.54-26.610.17561380.16282494X-RAY DIFFRACTION92.94
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)
10.8762202993220.220585421625-0.04956576196031.08543799478-0.2957575873520.7835980947610.0170607399208-0.0450534273374-0.0561207908906-0.0215664307097-0.0167883368430.05975192339280.0270539427881-0.0112060399108-0.001438346073450.1929347828890.00231304294021-0.008481539471240.282630338714-0.002694901488280.16272229684316.6150134708-0.7820073718160.40280438723
21.19826266999-0.154798185320.01647638947941.186747552170.3335726764041.4316539336-0.0122241391126-0.03673115819060.09098889236660.0580960263228-0.08230018407750.149596509295-0.108743280482-0.1119424546850.08308054774870.197604100161-0.0381656893713-0.01959733782710.290015283798-0.02073606397360.19604795140125.4820205319.537112129131.4771192585
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 425)AA22 - 4252 - 396
22(chain 'B' and resid 21 through 425)BB21 - 4251 - 396

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