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- PDB-7o0c: Human phosphomannomutase 2 (PMM2) wild-type in apo state -

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Basic information

Entry
Database: PDB / ID: 7o0c
TitleHuman phosphomannomutase 2 (PMM2) wild-type in apo state
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
Phosphomannomutase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRamon-Maiques, S. / Briso-Montiano, A. / Del Cano-Ochoa, F. / Vilas, A. / Perez, B. / Rubio, V.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-098084-B-100 Spain
Spanish Ministry of Economy and CompetitivenessPI19/01155 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
DepositionMar 26, 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)56,7048
Polymers56,5492
Non-polymers1566
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-60 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.582, 70.582, 360.801
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
11B-417-

HOH

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Components

#1: Protein Phosphomannomutase 2 / PMM 2


Mass: 28274.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM2 / Plasmid: pOPIN-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15305, phosphomannomutase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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 %
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 depoit 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 depoit 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97912 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.8→39.4 Å / Num. obs: 13763 / % possible obs: 96.5 % / Redundancy: 17.3 % / Biso Wilson estimate: 66.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.265 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 19 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2003 / CC1/2: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNAdata collection
PHENIX1.17.1_3660refinement
autoPROCdata processing
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AMY

2amy


Resolution: 2.8→39.4 Å / SU ML: 0.3794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 647 4.74 %
Rwork0.2169 12996 -
obs0.2193 13643 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 6 41 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893879
X-RAY DIFFRACTIONf_angle_d1.13825233
X-RAY DIFFRACTIONf_chiral_restr0.0704565
X-RAY DIFFRACTIONf_plane_restr0.0063687
X-RAY DIFFRACTIONf_dihedral_angle_d25.7502530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.37431270.29012578X-RAY DIFFRACTION99.74
3.02-3.320.34761260.24882627X-RAY DIFFRACTION99.89
3.32-3.80.24761090.22222314X-RAY DIFFRACTION87.35
3.8-4.790.2421270.18332574X-RAY DIFFRACTION95.37
4.79-39.40.25351580.21542903X-RAY DIFFRACTION99.9

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