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- PDB-8pno: The MgF3(H2O) transition state analog complex of E. coli YihX -

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Basic information

Entry
Database: PDB / ID: 8pno
TitleThe MgF3(H2O) transition state analog complex of E. coli YihX
ComponentsAlpha-D-glucose 1-phosphate phosphatase YihX
KeywordsHYDROLASE / phosphatase / HAD superfamily / transition state analog complex
Function / homology
Function and homology information


glucose-1-phosphatase / glucose-1-phosphatase activity / manganese ion binding / magnesium ion binding
Similarity search - Function
Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
IMIDAZOLE / trifluoromagnesate monohydrate / DI(HYDROXYETHYL)ETHER / Alpha-D-glucose 1-phosphate phosphatase YihX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaumann, P. / Zappala, D. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: The MgF3(H2O)- transition state analog complex of E. coli YihX
Authors: Baumann, P. / Zappala, D. / Jin, Y.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Nov 19, 2025Group: Non-polymer description / Structure summary / Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-D-glucose 1-phosphate phosphatase YihX
B: Alpha-D-glucose 1-phosphate phosphatase YihX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,48217
Polymers46,2782
Non-polymers1,20315
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-31 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.259, 79.325, 80.297
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-D-glucose 1-phosphate phosphatase YihX / Alpha-D-glucose-1-P phosphatase / Alpha-D-glucose-1-phosphatase / Haloacid dehalogenase-like ...Alpha-D-glucose-1-P phosphatase / Alpha-D-glucose-1-phosphatase / Haloacid dehalogenase-like phosphatase 4 / HAD4


Mass: 23139.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yihX, b3885, JW5566 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8Y3, glucose-1-phosphatase

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Non-polymers , 9 types, 246 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-KQB / trifluoromagnesate monohydrate


Mass: 99.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3H2MgO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.43 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 ...Details: 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000. The crystals are further soaked with the precipitant supplemented with 50 mM MgCl2 and 100 mM NH4F

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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: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→58.97 Å / Num. obs: 40811 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.992 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3532 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.31 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25711 2023 5 %RANDOM
Rwork0.21152 ---
obs0.21376 38765 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.56 Å2
2---3.87 Å2-0 Å2
3---3.74 Å2
Refinement stepCycle: 1 / Resolution: 2.2→59.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 111 231 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163025
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.654559
X-RAY DIFFRACTIONr_angle_other_deg0.4891.5697037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.552520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47110547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1834.0981602
X-RAY DIFFRACTIONr_mcbond_other3.1824.0991602
X-RAY DIFFRACTIONr_mcangle_it4.8026.1291999
X-RAY DIFFRACTIONr_mcangle_other4.8016.1322000
X-RAY DIFFRACTIONr_scbond_it3.7214.3421790
X-RAY DIFFRACTIONr_scbond_other3.7214.3421791
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4316.3792561
X-RAY DIFFRACTIONr_long_range_B_refined7.6951.5543848
X-RAY DIFFRACTIONr_long_range_B_other7.68951.5573849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 164 -
Rwork0.39 2852 -
obs--99.83 %

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