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- PDB-9qyy: MINPP1 from Bacteroides thetaiotaomicron R183 mutant -

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Basic information

Entry
Database: PDB / ID: 9qyy
TitleMINPP1 from Bacteroides thetaiotaomicron R183 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: 2.36 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)98,5134
Polymers98,3232
Non-polymers1902
Water4,125229
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2562
Polymers49,1611
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)49,2562
Polymers49,1611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.383, 119.123, 76.031
Angle α, β, γ (deg.)90.000, 107.960, 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: 49161.324 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
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: 2.36→30.76 Å / Num. obs: 36084 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 0.989 / Net I/σ(I): 7.58
Reflection shellResolution: 2.36→2.444 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.15 / Num. unique obs: 3566 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→30.76 Å / SU ML: 0.2055 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1801 4.99 %
Rwork0.1636 34283 -
obs0.1665 36084 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.17 Å2
Refinement stepCycle: LAST / Resolution: 2.36→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 10 229 6701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716650
X-RAY DIFFRACTIONf_angle_d0.86429000
X-RAY DIFFRACTIONf_chiral_restr0.0506962
X-RAY DIFFRACTIONf_plane_restr0.00781144
X-RAY DIFFRACTIONf_dihedral_angle_d5.522872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.420.23641140.18792625X-RAY DIFFRACTION98.38
2.42-2.490.25061410.18292635X-RAY DIFFRACTION98.27
2.49-2.570.2481230.18292589X-RAY DIFFRACTION97.94
2.57-2.670.23381470.17252607X-RAY DIFFRACTION98.22
2.67-2.770.21471260.17542681X-RAY DIFFRACTION98.73
2.77-2.90.23561470.17412594X-RAY DIFFRACTION98.42
2.9-3.050.25261400.18252636X-RAY DIFFRACTION99.04
3.05-3.240.21261480.17082624X-RAY DIFFRACTION98.93
3.24-3.490.24991360.16712653X-RAY DIFFRACTION99.15
3.49-3.840.19921480.1582624X-RAY DIFFRACTION99.11
3.84-4.40.19571470.14162660X-RAY DIFFRACTION99.15
4.4-5.530.18621410.14492653X-RAY DIFFRACTION99.43
5.54-30.760.24421430.16522702X-RAY DIFFRACTION99.06
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)
10.8005008936220.279735790185-0.06439500909730.881500767321-0.2060714555010.7067172002790.0242669700736-0.0362708144285-0.0476714519996-0.0279692473656-0.0188246185250.0609201677336-0.00937231302663-0.0268847299769-0.01009037989510.1561247629770.0112028128421-0.004473109880270.159125171014-0.01293178336560.14842100480416.4626398954-0.7976564685260.443376759036
20.907415635153-0.13113491849-0.008557139668220.7251843528290.2509834589181.00546406229-0.02022254632670.006272480881770.05990751958760.00686808452447-0.016860626880.0855612559227-0.0910485004789-0.008320800501110.0006396167867390.17617658861-0.0380624585998-0.005274059205220.16824746465-0.0001265157014830.15752796349125.530340700819.482169816531.4946343758
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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