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- PDB-6y8z: Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase ... -

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Basic information

Entry
Database: PDB / ID: 6y8z
TitleStructure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)
ComponentsPhosphoglucomutase 5
KeywordsISOMERASE / Phosphoglucomutase / Aciculin / binding partner / Low to no activity
Function / homology
Function and homology information


striated muscle tissue development / phosphoglucomutase activity / myofibril assembly / cell-substrate junction / adherens junction / sarcolemma / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Phosphoglucomutase / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Phosphoglucomutase-like protein 5
Similarity search - Component
Biological speciesClupea harengus (Atlantic herring)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGustafsson, R. / Eckhard, U. / Selmer, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationEvolution of new genes and proteins Sweden
CitationJournal: Biomolecules / Year: 2020
Title: Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding.
Authors: Gustafsson, R. / Eckhard, U. / Ye, W. / Enbody, E.D. / Pettersson, M. / Jemth, P. / Andersson, L. / Selmer, M.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucomutase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,64812
Polymers65,0301
Non-polymers61811
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-58 kcal/mol
Surface area22670 Å2
Unit cell
Length a, b, c (Å)47.200, 94.210, 146.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoglucomutase 5


Mass: 65029.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clupea harengus (Atlantic herring) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P3VN15*PLUS

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Non-polymers , 6 types, 390 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.0% (v/v) PEG 8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.05→48.9 Å / Num. obs: 38168 / % possible obs: 91.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.54 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.062 / Rrim(I) all: 0.14 / Net I/σ(I): 7.5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.023 / Mean I/σ(I) obs: 2 / Num. unique obs: 2184 / CC1/2: 0.429 / Rpim(I) all: 0.636 / Rrim(I) all: 1.222 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y8Y

6y8y


Resolution: 2.05→44.93 Å / SU ML: 0.3342 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2125
RfactorNum. reflection% reflection
Rfree0.2355 1924 5.08 %
Rwork0.1871 --
obs0.1896 37893 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 34 379 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234538
X-RAY DIFFRACTIONf_angle_d0.49566135
X-RAY DIFFRACTIONf_chiral_restr0.0442670
X-RAY DIFFRACTIONf_plane_restr0.0027808
X-RAY DIFFRACTIONf_dihedral_angle_d12.83182722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.4785950.47441685X-RAY DIFFRACTION60.96
2.1-2.160.34021420.29662742X-RAY DIFFRACTION97.53
2.16-2.220.28771310.25062719X-RAY DIFFRACTION97.8
2.22-2.290.33121110.28051866X-RAY DIFFRACTION66.14
2.29-2.380.27961810.21552692X-RAY DIFFRACTION97.69
2.38-2.470.25231380.19082784X-RAY DIFFRACTION98.42
2.47-2.580.22531520.18812759X-RAY DIFFRACTION98.38
2.58-2.720.25711190.20042359X-RAY DIFFRACTION83.32
2.72-2.890.24961410.17342796X-RAY DIFFRACTION98.79
2.89-3.110.22381260.17742846X-RAY DIFFRACTION98.74
3.11-3.430.22791420.1652829X-RAY DIFFRACTION98.21
3.43-3.920.20391400.14642206X-RAY DIFFRACTION81.49
3.92-4.940.18121510.12952773X-RAY DIFFRACTION97.73
4.94-44.930.21131550.19052913X-RAY DIFFRACTION94.96

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