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- PDB-9qyz: MINPP1 from Bacteroides thetaiotaomicron A31Y mutant -

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Basic information

Entry
Database: PDB / ID: 9qyz
TitleMINPP1 from Bacteroides thetaiotaomicron A31Y mutant
ComponentsMultiple inositol polyphosphate phosphatase 1
KeywordsHYDROLASE / Histidine phosphatase / phytase / mutant / complex
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / membrane
Similarity search - Function
Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Multiple inositol polyphosphate phosphatase 1
Similarity search - Component
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 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Structure summary / Category: struct / Item: _struct.title

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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)99,20911
Polymers98,5912
Non-polymers6189
Water7,891438
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5745
Polymers49,2961
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6366
Polymers49,2961
Non-polymers3405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.540, 115.120, 75.990
Angle α, β, γ (deg.)90.000, 107.920, 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: 49295.523 Da / Num. of mol.: 2 / Mutation: A31Y
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: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
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: I02 / Wavelength: 0.969 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.95→61.23 Å / Num. obs: 61493 / % possible obs: 98.39 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.86 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.17
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 6037 / CC1/2: 0.826

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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→61.23 Å / SU ML: 0.1842 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 3120 5.07 %
Rwork0.1517 58373 -
obs0.1533 61493 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 38 438 6974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816935
X-RAY DIFFRACTIONf_angle_d0.93549430
X-RAY DIFFRACTIONf_chiral_restr0.061008
X-RAY DIFFRACTIONf_plane_restr0.00851207
X-RAY DIFFRACTIONf_dihedral_angle_d5.7441961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.26671400.22142539X-RAY DIFFRACTION96.99
1.98-2.010.24441490.20212634X-RAY DIFFRACTION97.38
2.01-2.050.24571310.17822624X-RAY DIFFRACTION97.8
2.05-2.080.23541200.17152637X-RAY DIFFRACTION97.8
2.08-2.120.20051510.16422609X-RAY DIFFRACTION97.49
2.13-2.170.20131240.15962675X-RAY DIFFRACTION97.73
2.17-2.220.1831410.15692628X-RAY DIFFRACTION98.44
2.22-2.270.20171430.15552640X-RAY DIFFRACTION98.03
2.27-2.320.20781260.16162656X-RAY DIFFRACTION98.06
2.32-2.390.19511400.15622672X-RAY DIFFRACTION98.42
2.39-2.460.19161460.15862614X-RAY DIFFRACTION98.43
2.46-2.540.20291670.15312655X-RAY DIFFRACTION98.67
2.54-2.630.20121400.15012679X-RAY DIFFRACTION98.81
2.63-2.730.17851390.14662655X-RAY DIFFRACTION98.94
2.73-2.860.16931370.15012636X-RAY DIFFRACTION99.11
2.86-3.010.1941590.14962694X-RAY DIFFRACTION99.17
3.01-3.20.19091550.15492653X-RAY DIFFRACTION98.98
3.2-3.440.17421400.15232697X-RAY DIFFRACTION99.33
3.44-3.790.1491360.14182694X-RAY DIFFRACTION99.26
3.79-4.340.15541430.13232707X-RAY DIFFRACTION99.2
4.34-5.460.14751420.13452689X-RAY DIFFRACTION99.12
5.46-61.230.19971510.15992686X-RAY DIFFRACTION97.69
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)
10.7755225523660.1408686295070.1421018282420.812059222384-0.1166492452640.4229413008870.0581167249373-0.0946463985384-0.05728703861050.0253200199037-0.03962857176720.05980445025570.0462387220544-0.0355642300078-0.01488855180950.134888526313-0.00628007110339-0.00409886836220.1316686627670.002294767990820.10055126345416.5291651559-10.1765118663-0.00702251480184
20.959664347946-0.325480373341-0.1093434262010.6696591536680.1842666272140.681649604493-0.008449216577150.02532233029070.03204952657440.0297773047174-0.01722043396840.0663450805924-0.0367341833812-0.01600920519790.02823091045190.152773868386-0.0327193195142-0.004403077298920.156184807741-0.006762642252120.15293435254825.97598829.3253242900530.8809400218
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 21 - 426 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 21 through 426)AA - B
22(chain 'B' and resid 21 through 426)BC - D

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