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- PDB-9mmi: Myo-inositol-1(or 4)-monophosphatase that can perform essential d... -

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Basic information

Entry
Database: PDB / ID: 9mmi
TitleMyo-inositol-1(or 4)-monophosphatase that can perform essential dephosphorylation step to facilitate riboflavin biosynthesis
ComponentsFructose-1,6-bisphosphatase/inositol-1-monophosphatase
KeywordsHYDROLASE / riboflavin / phosphatase
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / signal transduction / metal ion binding
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
PHOSPHATE ION / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHoffpauir, Z.A. / Meneely, K.M. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204080 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Identification of the phosphatase essential for riboflavin biosynthesis in Aquifex aeolicus.
Authors: Hoffpauir, Z.A. / Lamb, A.L.
History
DepositionDec 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
B: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
C: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
D: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,93923
Polymers117,4924
Non-polymers1,44819
Water5,801322
1
A: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
B: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,97816
Polymers58,7462
Non-polymers1,23314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-158 kcal/mol
Surface area18960 Å2
MethodPISA
2
C: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
D: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9617
Polymers58,7462
Non-polymers2155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-66 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.190, 72.914, 119.245
Angle α, β, γ (deg.)90.000, 90.030, 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
Fructose-1,6-bisphosphatase/inositol-1-monophosphatase / FBPase/IMPase / Inositol-1-phosphatase / I-1-Pase


Mass: 29372.885 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: suhB, imp2, aq_1983 / Production host: Escherichia coli (E. coli)
References: UniProt: O67791, fructose-bisphosphatase, inositol-phosphate phosphatase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.75 mM HEPES pH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→37.68 Å / Num. obs: 110871 / % possible obs: 98.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.19 Å2 / Rpim(I) all: 0.034 / Net I/σ(I): 11.3
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5264 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→37.68 Å / SU ML: 0.1401 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 2007 1.81 %
Rwork0.1823 108778 -
obs0.1827 110785 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.65 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7760 0 90 322 8172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01218022
X-RAY DIFFRACTIONf_angle_d1.251910812
X-RAY DIFFRACTIONf_chiral_restr0.06751157
X-RAY DIFFRACTIONf_plane_restr0.01491362
X-RAY DIFFRACTIONf_dihedral_angle_d16.96122928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.28941340.25887455X-RAY DIFFRACTION94.9
1.79-1.840.25281420.22497700X-RAY DIFFRACTION98.25
1.84-1.90.21291400.20237747X-RAY DIFFRACTION98.6
1.9-1.960.21511470.18837781X-RAY DIFFRACTION98.68
1.96-2.030.21191450.18817844X-RAY DIFFRACTION98.92
2.03-2.110.18451440.18147712X-RAY DIFFRACTION98.71
2.11-2.20.20191460.17447810X-RAY DIFFRACTION99.08
2.2-2.320.23141410.18197806X-RAY DIFFRACTION98.87
2.32-2.470.16531440.17687721X-RAY DIFFRACTION98.07
2.47-2.660.19721440.17947602X-RAY DIFFRACTION95.9
2.66-2.920.20881430.18867900X-RAY DIFFRACTION99.86
2.92-3.350.22851470.18097909X-RAY DIFFRACTION99.78
3.35-4.220.17871420.16227924X-RAY DIFFRACTION99.41
4.22-37.680.22761480.18737867X-RAY DIFFRACTION97.09

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