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- PDB-7o4g: Human phosphomannomutase 2 (PMM2) wild-type soaked with the activ... -

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Basic information

Entry
Database: PDB / ID: 7o4g
TitleHuman phosphomannomutase 2 (PMM2) wild-type soaked with the activator glucose 1,6-bisphosphate
ComponentsPhosphomannomutase 2
KeywordsISOMERASE / glycobiology / congenital disorders of glycosylation / phosphotransferase / phosphomutase
Function / homology
Function and homology information


Defective PMM2 causes PMM2-CDG / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / neuronal cell body / nucleoplasm ...Defective PMM2 causes PMM2-CDG / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / 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: 2.66 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 6, 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

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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)57,13610
Polymers56,5492
Non-polymers5878
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-54 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.144, 71.144, 361.266
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-430-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Phosphomannomutase 2 / / PMM 2


Mass: 28274.336 Da / Num. of mol.: 2
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
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM2 / Plasmid: pOPIN-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15305, phosphomannomutase
#5: 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 / Glucose 1,6-bisphosphate


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, 82 molecules

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


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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 46.5 %
Description: Crystals of hexagonal morphology and 0.025 mm in the largest dimension
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 in 20 mM Hepes pH 7.5 and 0.2 M NaCl. ...Details: Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein 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. Crystals were soaked for 5-10 min in mother liquor with 6 mM glucose 1,6-bisphophate.

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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: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.66→361.27 Å / Num. obs: 16779 / % possible obs: 100 % / Redundancy: 25.3 % / Biso Wilson estimate: 52.66 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.417 / Rpim(I) all: 0.085 / Net I/σ(I): 9.2
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 26.7 % / Rmerge(I) obs: 3.011 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2150 / CC1/2: 0.625 / Rpim(I) all: 0.813 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNAdata collection
AutoProcessdata extraction
PHENIXv1.19refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0C

7o0c


Resolution: 2.66→60.21 Å / SU ML: 0.2639 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 861 5.17 %
Rwork0.2235 15802 -
obs0.2261 16663 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.98 Å2
Refinement stepCycle: LAST / Resolution: 2.66→60.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 32 75 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893952
X-RAY DIFFRACTIONf_angle_d1.03265337
X-RAY DIFFRACTIONf_chiral_restr0.0536574
X-RAY DIFFRACTIONf_plane_restr0.0091699
X-RAY DIFFRACTIONf_dihedral_angle_d5.3252542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.830.30251460.24552539X-RAY DIFFRACTION100
2.83-3.040.34311420.27852548X-RAY DIFFRACTION100
3.05-3.350.30781350.24612574X-RAY DIFFRACTION99.89
3.35-3.840.28951240.22372623X-RAY DIFFRACTION99.93
3.84-4.830.21651520.17762650X-RAY DIFFRACTION100
4.83-60.210.27881620.23432868X-RAY DIFFRACTION99.9

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