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- PDB-7o58: Human phosphomannomutase 2 (PMM2) with mutation T237M in complex ... -

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Basic information

Entry
Database: PDB / ID: 7o58
TitleHuman phosphomannomutase 2 (PMM2) with mutation T237M in complex with the activator glucose 1,6-bisphosphate
ComponentsPhosphomannomutase 2
KeywordsISOMERASE / glycobiology / congenital disorders of glycosylation / phosphotransferase / phosphomutase
Function / homology
Function and homology information


GDP-D-mannose biosynthetic process from fructose-6-phosphate / Defective PMM2 causes PMM2-CDG / GDP-mannose biosynthetic process from mannose / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / : ...GDP-D-mannose biosynthetic process from fructose-6-phosphate / Defective PMM2 causes PMM2-CDG / GDP-mannose biosynthetic process from mannose / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / : / microtubule cytoskeleton / cilium / neuronal cell body / nucleoplasm / metal ion binding / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRamon-Maiques, S. / Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Perez, B. / Rubio, V.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-098084-B-100 Spain
Spanish Ministry of Economy and CompetitivenessPI19/01155 Spain
CitationJournal: J Inherit Metab Dis / Year: 2022
Title: Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures.
Authors: Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Velazquez-Campoy, A. / Rubio, V. / Perez, B. / Ramon-Maiques, S.
History
DepositionApr 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,97820
Polymers56,6092
Non-polymers1,37018
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-73 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.520, 70.520, 359.720
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-410-

NA

21A-554-

HOH

31A-579-

HOH

41B-673-

HOH

51B-728-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Phosphomannomutase 2 / PMM 2


Mass: 28304.428 Da / Num. of mol.: 2 / Mutation: T237M
Source method: isolated from a genetically manipulated source
Details: Residues GPMAAP at the N-terminus are not seen in the electron density map. The most N-terminal GP sequence is part of the fusion tag after cleavage Protein has mutation T237M
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM2 / Plasmid: pOPIN-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15305, phosphomannomutase
#3: 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.: 1 / 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, 314 molecules

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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein and 3 mM glucose 1,6-bisphophate in 20 ...Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein and 3 mM glucose 1,6-bisphophate in 20 mM Hepes pH 7.5 and 0.2 M NaCl. Crystallization solution contained 0.3-0.4 M MgCl2, 24% PEG3350 and 0.1 M HEPES pH 7.5

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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: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.965→59.95 Å / Num. obs: 37985 / % possible obs: 96.4 % / Redundancy: 18.3 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.042 / Net I/σ(I): 14.7
Reflection shellResolution: 1.965→2.01 Å / Redundancy: 19.2 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2683 / CC1/2: 0.751 / Rpim(I) all: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNA1.19.2_4158data collection
PHENIX1.19.2_4158refinement
AutoProcessdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0C

7o0c


Resolution: 1.97→59.95 Å / SU ML: 0.1822 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 1894 5.01 %
Rwork0.1827 35929 -
obs0.1851 37823 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.5 Å2
Refinement stepCycle: LAST / Resolution: 1.97→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 82 297 4257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01444104
X-RAY DIFFRACTIONf_angle_d1.21525527
X-RAY DIFFRACTIONf_chiral_restr0.0654583
X-RAY DIFFRACTIONf_plane_restr0.0112721
X-RAY DIFFRACTIONf_dihedral_angle_d8.4912573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.29951500.2382560X-RAY DIFFRACTION99.96
2.01-2.070.26731520.22072570X-RAY DIFFRACTION99.96
2.07-2.130.25791360.21052585X-RAY DIFFRACTION99.93
2.13-2.20.24191330.18782626X-RAY DIFFRACTION99.96
2.2-2.280.2818690.21511285X-RAY DIFFRACTION49.56
2.28-2.370.26041410.1782594X-RAY DIFFRACTION99.93
2.37-2.480.22081130.17862625X-RAY DIFFRACTION99.96
2.48-2.610.21351360.18022655X-RAY DIFFRACTION100
2.61-2.770.23581070.19322662X-RAY DIFFRACTION99.96
2.77-2.980.27941380.20082658X-RAY DIFFRACTION99.96
2.98-3.280.22061570.18322660X-RAY DIFFRACTION99.96
3.28-3.760.22861540.1712697X-RAY DIFFRACTION99.96
3.76-4.740.18241550.14432766X-RAY DIFFRACTION100
4.74-59.950.23841530.20022986X-RAY DIFFRACTION99.87

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