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- PDB-9qz3: MINPP1 from Bacteroides thetaiotaomicron T30I mutant complex with... -

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Basic information

Entry
Database: PDB / ID: 9qz3
TitleMINPP1 from Bacteroides thetaiotaomicron T30I 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: 1.8 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)99,7524
Polymers98,4312
Non-polymers1,3212
Water8,935496
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8762
Polymers49,2151
Non-polymers6611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8762
Polymers49,2151
Non-polymers6611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.851, 114.166, 75.483
Angle α, β, γ (deg.)90.000, 107.370, 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: 49215.480 Da / Num. of mol.: 2 / Mutation: T30I
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) / 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.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
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: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→60.93 Å / Num. obs: 77466 / % possible obs: 99.61 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.31 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.38
Reflection shellResolution: 1.8→1.864 Å / Mean I/σ(I) obs: 1.75 / Num. unique obs: 7551 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→60.93 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 3804 4.93 %
Rwork0.1832 73369 -
obs0.1847 77173 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→60.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 72 496 7084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00846845
X-RAY DIFFRACTIONf_angle_d0.94979303
X-RAY DIFFRACTIONf_chiral_restr0.05661009
X-RAY DIFFRACTIONf_plane_restr0.00791168
X-RAY DIFFRACTIONf_dihedral_angle_d6.8923942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31061390.30992570X-RAY DIFFRACTION96.17
1.82-1.850.34611330.29512753X-RAY DIFFRACTION99.07
1.85-1.870.34361390.27252701X-RAY DIFFRACTION99.4
1.87-1.90.30581670.25512651X-RAY DIFFRACTION99.19
1.9-1.930.28491380.24752737X-RAY DIFFRACTION99.52
1.93-1.960.27491460.22992663X-RAY DIFFRACTION99.26
1.96-1.990.24541680.21162731X-RAY DIFFRACTION99.72
1.99-2.020.23721420.20792654X-RAY DIFFRACTION99.75
2.02-2.060.25641300.2062741X-RAY DIFFRACTION99.72
2.06-2.10.2371140.19722735X-RAY DIFFRACTION99.51
2.1-2.140.22671320.18432730X-RAY DIFFRACTION99.97
2.14-2.190.23041270.1882715X-RAY DIFFRACTION99.79
2.19-2.240.23061500.18312716X-RAY DIFFRACTION99.86
2.24-2.30.1921400.18222730X-RAY DIFFRACTION99.9
2.3-2.360.22381160.17572786X-RAY DIFFRACTION99.79
2.36-2.430.2161640.1752639X-RAY DIFFRACTION99.68
2.43-2.510.2361470.17642729X-RAY DIFFRACTION99.9
2.51-2.60.21191460.18042743X-RAY DIFFRACTION99.83
2.6-2.70.24861250.17452703X-RAY DIFFRACTION99.75
2.7-2.820.18771460.17142705X-RAY DIFFRACTION99.82
2.82-2.970.21531330.17152749X-RAY DIFFRACTION99.93
2.97-3.160.21481600.16922716X-RAY DIFFRACTION100
3.16-3.40.16891590.17092711X-RAY DIFFRACTION100
3.4-3.740.18961280.16542763X-RAY DIFFRACTION100
3.74-4.280.20191310.16782760X-RAY DIFFRACTION99.93
4.29-5.40.16131510.15932733X-RAY DIFFRACTION100
5.4-60.930.22491330.18582805X-RAY DIFFRACTION99.86
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)
10.3558978130050.03300261402140.006882089762460.262070925755-0.1113114935370.2367275230620.0247694258545-0.0520098523342-0.00691796788007-0.0112121083647-0.01903585749090.01028446653960.00321330932622-0.012208330025-4.9457258773E-60.160210897359-0.00192846517168-0.005532902546940.1416657654740.00783602368960.141793352694119.972373965-5.895672665130.149047864
20.352794190494-0.0269956574629-0.08099407408690.1429916481050.1195479897480.2823142924270.009916806233560.01961006520280.0219782680657-0.00490784781459-0.0240605922629-0.00570225481715-0.000883257439179-0.00301889030812-6.45321345082E-60.152713494650.003045409654740.0006385719072640.151494298618-0.01132810509650.147570521496129.48636533113.437583191830.6657331611
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 19 - 424 / Label seq-ID: 1 - 399

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 19 through 424)AA
22(chain 'B' and resid 19 through 424)BB

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