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- PDB-5jn5: Crystal structure of the D263Y missense variant of human PGM1 -

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Basic information

Entry
Database: PDB / ID: 5jn5
TitleCrystal structure of the D263Y missense variant of human PGM1
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / phosphohexomutase / enzyme
Function / homology
Function and homology information


Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / Neutrophil degranulation / magnesium ion binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Phosphoglucomutase / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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, conserved site ...Phosphoglucomutase / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / 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 / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsBeamer, L.J. / Stiers, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0918389 United States
CitationJournal: FEBS J. / Year: 2017
Title: Asp263 missense variants perturb the active site of human phosphoglucomutase 1.
Authors: Stiers, K.M. / Graham, A.C. / Kain, B.N. / Beamer, L.J.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Nov 27, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucomutase-1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,39211
Polymers128,6402
Non-polymers7539
Water25,6351423
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7446
Polymers64,3201
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6485
Polymers64,3201
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.988, 172.988, 100.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

21A-1447-

HOH

Detailsdimer according to dynamic light scattering

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Components

#1: Protein Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1


Mass: 64319.805 Da / Num. of mol.: 2 / Mutation: D263Y
Source method: isolated from a genetically manipulated source
Details: Phosphoserine at residue 117 / Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1423 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: LITHIUM OR AMMONIUM SULFATE (1.4 - 1.55 M) WITH 0.1 M TRIS, PH 7.5 OR MES PH 6.0
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.75→57.7 Å / Num. obs: 151916 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.587 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 1.75→54.704 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.94
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 7553 4.98 %matched WT data set
Rwork0.1799 ---
obs0.1814 151818 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→54.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8415 0 37 1423 9875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088771
X-RAY DIFFRACTIONf_angle_d1.08911939
X-RAY DIFFRACTIONf_dihedral_angle_d12.593167
X-RAY DIFFRACTIONf_chiral_restr0.0471348
X-RAY DIFFRACTIONf_plane_restr0.0061560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.30412410.27564737X-RAY DIFFRACTION100
1.7699-1.79070.25052300.25094751X-RAY DIFFRACTION100
1.7907-1.81260.28932620.25514769X-RAY DIFFRACTION100
1.8126-1.83550.30032390.24264776X-RAY DIFFRACTION100
1.8355-1.85970.27772180.23864766X-RAY DIFFRACTION100
1.8597-1.88510.27872310.23024821X-RAY DIFFRACTION100
1.8851-1.91210.2352540.22044707X-RAY DIFFRACTION100
1.9121-1.94060.26152560.2144766X-RAY DIFFRACTION100
1.9406-1.97090.24652390.20064770X-RAY DIFFRACTION100
1.9709-2.00320.23052370.20284776X-RAY DIFFRACTION100
2.0032-2.03780.25022350.19724813X-RAY DIFFRACTION100
2.0378-2.07480.22332430.19524755X-RAY DIFFRACTION100
2.0748-2.11480.20482790.194757X-RAY DIFFRACTION100
2.1148-2.15790.20492480.19014757X-RAY DIFFRACTION100
2.1579-2.20480.23172480.18594797X-RAY DIFFRACTION100
2.2048-2.25610.20772620.18234750X-RAY DIFFRACTION100
2.2561-2.31260.21752770.17934770X-RAY DIFFRACTION100
2.3126-2.37510.20182360.17714824X-RAY DIFFRACTION100
2.3751-2.4450.2072400.17284801X-RAY DIFFRACTION100
2.445-2.52390.21012810.1734756X-RAY DIFFRACTION100
2.5239-2.61410.21182480.17554814X-RAY DIFFRACTION100
2.6141-2.71880.20752740.17594774X-RAY DIFFRACTION100
2.7188-2.84250.21152570.18124845X-RAY DIFFRACTION100
2.8425-2.99230.20442490.18234810X-RAY DIFFRACTION100
2.9923-3.17980.20072570.17514866X-RAY DIFFRACTION100
3.1798-3.42530.22052560.17074835X-RAY DIFFRACTION100
3.4253-3.76990.1742610.15394881X-RAY DIFFRACTION100
3.7699-4.31520.1732440.14884915X-RAY DIFFRACTION100
4.3152-5.43590.17912870.15084920X-RAY DIFFRACTION100
5.4359-54.73030.19592640.18385186X-RAY DIFFRACTION100

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