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- PDB-9hn3: Mouse phosphomannomutase 2 in apo state from crystals with PEG 3350 -

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Basic information

Entry
Database: PDB / ID: 9hn3
TitleMouse phosphomannomutase 2 in apo state from crystals with PEG 3350
ComponentsPhosphomannomutase 2
KeywordsISOMERASE / N-glycosylation / congenital disorder of glycosylation / carbohydrate-deficient / hypoglycosylation / homodimer / phosphoglucomutase / nucleotide-sugar biosynthesis / mannose-1-phosphate / GDP-mannose
Function / homology
Function and homology information


Synthesis of GDP-mannose / GDP-D-mannose biosynthetic process from fructose-6-phosphate / GDP-mannose biosynthetic process from mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / microtubule cytoskeleton / cilium / neuronal cell body / nucleoplasm ...Synthesis of GDP-mannose / GDP-D-mannose biosynthetic process from fructose-6-phosphate / GDP-mannose biosynthetic process from mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / microtubule cytoskeleton / cilium / neuronal cell body / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Phosphomannomutase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsDel Cano-Ochoa, F. / Vilar, M. / Vilas, A. / Company, R. / Perez, B. / Ramon-Maiques, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTI2018-098084-B-100 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-128468NB-I00 Spain
CitationJournal: To Be Published
Title: High conformational flexibility of phosphomannomutase 2: Implications for functioning mechanisms, stability and pharmacological chaperone design
Authors: Del Cano-Ochoa, F. / Vilar, M. / Vilas, A. / Company, R. / Perez, B. / Ramon-Maiques, S.
History
DepositionDec 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomannomutase 2
B: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25516
Polymers55,6982
Non-polymers55814
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-126 kcal/mol
Surface area22280 Å2
Unit cell
Length a, b, c (Å)71.811, 71.811, 355.897
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-306-

CL

21B-483-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphomannomutase 2 / PMM 2


Mass: 27848.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: First two amino acids, "GP", remain from the fusion tag after protease cleavage.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pmm2 / Plasmid: pOPIN-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z2M7, phosphomannomutase

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Non-polymers , 6 types, 632 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Best crystals appeared after 2-7 days using 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, and 27-30% PEG 3350 as reservoir, in hanging drop 24-well plates, by mixing 2 ul of protein with 2 ul of reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.49→177.95 Å / Num. obs: 89547 / % possible obs: 99.3 % / Redundancy: 19.2 % / Biso Wilson estimate: 25.03 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 16.7
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 19.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4298 / CC1/2: 0.591 / Rpim(I) all: 0.627 / % possible all: 98.2

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Processing

Software
NameVersionClassification
AutoProcessdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→62.19 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 4607 5.15 %
Rwork0.1791 84843 -
obs0.1799 89450 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.74 Å2
Refinement stepCycle: LAST / Resolution: 1.49→62.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 24 618 4532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534137
X-RAY DIFFRACTIONf_angle_d0.71025591
X-RAY DIFFRACTIONf_chiral_restr0.0606587
X-RAY DIFFRACTIONf_plane_restr0.0058742
X-RAY DIFFRACTIONf_dihedral_angle_d5.8941579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.3241470.33152746X-RAY DIFFRACTION97.7
1.51-1.520.28871470.2782745X-RAY DIFFRACTION97.8
1.52-1.540.24491410.2532708X-RAY DIFFRACTION97.87
1.54-1.560.26851570.25482779X-RAY DIFFRACTION98.06
1.56-1.580.28361470.31612727X-RAY DIFFRACTION98.16
1.58-1.60.30191280.32442755X-RAY DIFFRACTION97.99
1.6-1.630.30281520.28472781X-RAY DIFFRACTION98.39
1.63-1.650.30011550.25652726X-RAY DIFFRACTION98.23
1.65-1.680.24891460.22662773X-RAY DIFFRACTION98.32
1.68-1.70.25431430.22322796X-RAY DIFFRACTION98.39
1.7-1.730.23261430.21872739X-RAY DIFFRACTION98.66
1.73-1.770.23131460.20362779X-RAY DIFFRACTION98.62
1.77-1.80.2191620.20682815X-RAY DIFFRACTION98.67
1.8-1.840.18521540.19372774X-RAY DIFFRACTION98.82
1.84-1.880.191410.1972790X-RAY DIFFRACTION98.79
1.88-1.920.19371530.19742795X-RAY DIFFRACTION98.89
1.92-1.970.22291540.20442800X-RAY DIFFRACTION99.13
1.97-2.020.20711620.21122817X-RAY DIFFRACTION99.13
2.02-2.080.18651610.19632796X-RAY DIFFRACTION99.1
2.08-2.150.20421710.1852819X-RAY DIFFRACTION99.43
2.15-2.220.20271460.17622851X-RAY DIFFRACTION99.27
2.22-2.310.20571550.1712865X-RAY DIFFRACTION99.47
2.31-2.420.18241570.17252836X-RAY DIFFRACTION99.73
2.42-2.550.17071530.1772879X-RAY DIFFRACTION99.67
2.55-2.710.17771630.18432874X-RAY DIFFRACTION99.74
2.71-2.910.18351500.1722911X-RAY DIFFRACTION99.97
2.91-3.210.17711800.16232904X-RAY DIFFRACTION99.94
3.21-3.670.17741610.15522974X-RAY DIFFRACTION99.94
3.67-4.630.16221560.13543033X-RAY DIFFRACTION100
4.63-62.190.22041760.18643256X-RAY DIFFRACTION99.74

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