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- PDB-6y8x: Structure of Atlantic Herring (Clupea Harengus) Phosphoglucomutas... -

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Basic information

Entry
Database: PDB / ID: 6y8x
TitleStructure of Atlantic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)
ComponentsPhosphoglucomutase 5
KeywordsISOMERASE / Phosphoglucomutase / Aciculin / binding partner / Low to no activity
Biological speciesClupea harengus (Atlantic herring)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
AA: Phosphoglucomutase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5253
Polymers62,4621
Non-polymers632
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-15 kcal/mol
Surface area22970 Å2
Unit cell
Length a, b, c (Å)59.210, 86.220, 63.520
Angle α, β, γ (deg.)90.000, 109.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Phosphoglucomutase 5


Mass: 62462.250 Da / Num. of mol.: 1 / Mutation: V330A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clupea harengus (Atlantic herring) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0 M sodium malonate pH 6.0, 0.1 M MES pH 6.0, 1.0% (v/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→55.98 Å / Num. obs: 28235 / % possible obs: 98.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 25.58 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.171 / Rrim(I) all: 0.289 / Net I/σ(I): 3.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2607 / CC1/2: 0.221 / Rpim(I) all: 0.648 / Rrim(I) all: 1.102 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
MOSFLMdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.25→55.98 Å / SU ML: 0.4211 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.4579
RfactorNum. reflection% reflection
Rfree0.2884 1371 4.87 %
Rwork0.2368 --
obs0.2394 28178 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.59 Å2
Refinement stepCycle: LAST / Resolution: 2.25→55.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 2 216 4555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224424
X-RAY DIFFRACTIONf_angle_d0.47325983
X-RAY DIFFRACTIONf_chiral_restr0.0433658
X-RAY DIFFRACTIONf_plane_restr0.0033790
X-RAY DIFFRACTIONf_dihedral_angle_d14.79842655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.35041570.33452670X-RAY DIFFRACTION98.26
2.33-2.420.35371320.32992631X-RAY DIFFRACTION97.84
2.42-2.530.41791170.30682694X-RAY DIFFRACTION97.98
2.53-2.670.39061370.30482664X-RAY DIFFRACTION97.56
2.67-2.830.34581550.27822654X-RAY DIFFRACTION98.53
2.83-3.050.32461280.26982691X-RAY DIFFRACTION98.15
3.05-3.360.27621280.23112681X-RAY DIFFRACTION97.98
3.36-3.850.25621320.20022696X-RAY DIFFRACTION98.23
3.85-4.850.20211480.15582691X-RAY DIFFRACTION98.2
4.85-55.980.26481370.21132735X-RAY DIFFRACTION97.75

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