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- PDB-9i55: Mouse phosphomannomutase 2 in complex with the activator glucose-... -

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Basic information

Entry
Database: PDB / ID: 9i55
TitleMouse phosphomannomutase 2 in complex with the activator glucose-1,6-bisphosphate
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 / cytosol / cytoplasm
Similarity search - Function
Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphomannomutase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionJan 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: 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
D: Phosphomannomutase 2
F: Phosphomannomutase 2
C: Phosphomannomutase 2
E: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,99828
Polymers167,0936
Non-polymers1,90522
Water5,296294
1
A: Phosphomannomutase 2
B: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32011
Polymers55,6982
Non-polymers6229
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-44 kcal/mol
Surface area22000 Å2
MethodPISA
2
D: Phosphomannomutase 2
C: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4738
Polymers55,6982
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-34 kcal/mol
Surface area22070 Å2
MethodPISA
3
F: Phosphomannomutase 2
E: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2059
Polymers55,6982
Non-polymers5077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-61 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.285, 99.138, 213.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 10 molecules ABDFCE

#1: Protein
Phosphomannomutase 2 / PMM 2


Mass: 27848.814 Da / Num. of mol.: 6
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
#6: Sugar
ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 312 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: Drops of 2 ul of protein and 2 mM glucose-1,6-bisphosphate (Sigma) and 2 ul of reservoir solution. Best crystals appeared after 2-7 days in 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 20-22% PEG ...Details: Drops of 2 ul of protein and 2 mM glucose-1,6-bisphosphate (Sigma) and 2 ul of reservoir solution. Best crystals appeared after 2-7 days in 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 20-22% PEG 8000. Crystals were cryo-protected by briefly soaking in mother liquor with increasing concentrations of PEG up to 30% and 5% glycerol.

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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: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→213.47 Å / Num. obs: 45273 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 61.1 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.097 / Net I/σ(I): 6.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4408 / CC1/2: 0.558 / Rpim(I) all: 0.883 / % possible all: 100

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Processing

Software
NameVersionClassification
AutoProcess1.20.1_4487data processing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→64.67 Å / SU ML: 0.4747 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 30.2492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 4319 5.05 %
Rwork0.2054 81247 -
obs0.2084 45273 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.48 Å2
Refinement stepCycle: LAST / Resolution: 2.75→64.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11503 0 103 294 11900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004711829
X-RAY DIFFRACTIONf_angle_d0.68515954
X-RAY DIFFRACTIONf_chiral_restr0.04271712
X-RAY DIFFRACTIONf_plane_restr0.01292076
X-RAY DIFFRACTIONf_dihedral_angle_d5.59071598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.780.40961340.34912741X-RAY DIFFRACTION99.86
2.78-2.810.3951490.33932702X-RAY DIFFRACTION99.86
2.81-2.850.30191480.33612758X-RAY DIFFRACTION99.69
2.85-2.880.3451350.33912722X-RAY DIFFRACTION99.55
2.88-2.920.39351670.33152748X-RAY DIFFRACTION99.76
2.92-2.960.39811160.32022719X-RAY DIFFRACTION99.89
2.96-30.37731410.31972796X-RAY DIFFRACTION99.86
3-3.050.4011260.30852738X-RAY DIFFRACTION99.9
3.05-3.10.37461520.30092737X-RAY DIFFRACTION99.9
3.1-3.150.34991300.2912744X-RAY DIFFRACTION99.79
3.15-3.20.31821370.26812753X-RAY DIFFRACTION99.9
3.2-3.260.31191370.27222725X-RAY DIFFRACTION100
3.26-3.320.31341480.26982754X-RAY DIFFRACTION100
3.32-3.390.27741560.26252738X-RAY DIFFRACTION99.83
3.39-3.460.30891370.23982750X-RAY DIFFRACTION99.79
3.46-3.550.27751360.22612756X-RAY DIFFRACTION99.86
3.55-3.630.25771720.20192673X-RAY DIFFRACTION99.82
3.63-3.730.32151630.20162741X-RAY DIFFRACTION99.86
3.73-3.840.27471630.18652698X-RAY DIFFRACTION99.79
3.84-3.970.25261050.18651891X-RAY DIFFRACTION68.99
3.97-4.110.23531440.16972740X-RAY DIFFRACTION99.97
4.11-4.270.27721510.1562768X-RAY DIFFRACTION99.9
4.27-4.470.2161260.15862735X-RAY DIFFRACTION99.97
4.47-4.70.19231560.14982735X-RAY DIFFRACTION99.97
4.7-50.24031430.14662736X-RAY DIFFRACTION99.86
5-5.380.22841260.16172749X-RAY DIFFRACTION99.93
5.38-5.920.21391800.18172709X-RAY DIFFRACTION99.93
5.92-6.780.22411430.19412748X-RAY DIFFRACTION99.9
6.78-8.540.21561220.18062760X-RAY DIFFRACTION99.9
8.54-64.670.22081760.15542683X-RAY DIFFRACTION99.2

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