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- PDB-9hpb: Mouse phosphomannomutase 2 in apo state from crystals with PEG 8000 -

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Basic information

Entry
Database: PDB / ID: 9hpb
TitleMouse phosphomannomutase 2 in apo state from crystals with PEG 8000
ComponentsPhosphomannomutase 2
KeywordsISOMERASE / N-glycosylation / congenital disorder of glycosylation / carbohydrate-deficient / hypoglycosylation / homodimer / phosphoglucomutase / nucleotide-sugar biosynthesis / mannose-1-phosphate / GDP-mannose / ISOMERAS
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: 2.43 Å
AuthorsRamon-Maiques, S. / Del Cano-Ochoa, F. / Company, R.
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-100 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 12, 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
D: Phosphomannomutase 2
F: Phosphomannomutase 2
C: Phosphomannomutase 2
E: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,59425
Polymers167,0936
Non-polymers50119
Water5,711317
1
A: Phosphomannomutase 2
B: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8538
Polymers55,6982
Non-polymers1566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Phosphomannomutase 2
C: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91010
Polymers55,6982
Non-polymers2138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Phosphomannomutase 2
E: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8307
Polymers55,6982
Non-polymers1335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.657, 98.611, 212.849
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

#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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: Best crystals appeared after 2-7 days using 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, and 20-22% PEG 8000 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: 2.43→106.43 Å / Num. obs: 64543 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.11 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.046 / Net I/σ(I): 10.6
Reflection shellResolution: 2.43→2.48 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3193 / CC1/2: 0.614 / Rpim(I) all: 0.873 / % possible all: 99.9

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Processing

Software
NameVersionClassification
autoPROC1.20.1_4487data processing
XDS1.20.1_4487data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→53.21 Å / SU ML: 0.4023 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.1185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2705 3146 4.88 %
Rwork0.234 61330 -
obs0.2359 64476 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.09 Å2
Refinement stepCycle: LAST / Resolution: 2.43→53.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11421 0 19 317 11757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004311666
X-RAY DIFFRACTIONf_angle_d0.622315730
X-RAY DIFFRACTIONf_chiral_restr0.04171686
X-RAY DIFFRACTIONf_plane_restr0.01552070
X-RAY DIFFRACTIONf_dihedral_angle_d5.46491586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.470.43621580.38242726X-RAY DIFFRACTION99.45
2.47-2.510.35231290.37462749X-RAY DIFFRACTION99.93
2.51-2.550.39451330.3632774X-RAY DIFFRACTION99.83
2.55-2.60.40791400.36082777X-RAY DIFFRACTION99.79
2.6-2.650.37011430.33862695X-RAY DIFFRACTION99.72
2.65-2.710.47111260.38252786X-RAY DIFFRACTION99.79
2.71-2.760.43511380.3572774X-RAY DIFFRACTION99.9
2.76-2.830.35531570.33462728X-RAY DIFFRACTION99.83
2.83-2.90.34191360.3032773X-RAY DIFFRACTION99.69
2.9-2.980.35641290.28242766X-RAY DIFFRACTION99.9
2.98-3.070.30551480.27392763X-RAY DIFFRACTION99.97
3.07-3.160.27641340.26942777X-RAY DIFFRACTION99.97
3.16-3.280.26581430.27972772X-RAY DIFFRACTION99.93
3.28-3.410.30421430.26992769X-RAY DIFFRACTION99.93
3.41-3.560.2731500.2362788X-RAY DIFFRACTION99.93
3.56-3.750.27061430.20992783X-RAY DIFFRACTION99.97
3.75-3.990.24031400.20852810X-RAY DIFFRACTION99.8
3.99-4.290.25041500.19452799X-RAY DIFFRACTION99.86
4.29-4.730.20931550.1732827X-RAY DIFFRACTION99.97
4.73-5.410.20831250.17672840X-RAY DIFFRACTION99.93
5.41-6.810.23861570.22292861X-RAY DIFFRACTION99.97
6.81-53.210.24651690.20192993X-RAY DIFFRACTION99.68

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