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- PDB-7s77: Crystal structure of the G391V variant of human PGM-1 -

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Basic information

Entry
Database: PDB / ID: 7s77
TitleCrystal structure of the G391V variant of human PGM-1
ComponentsPhosphoglucomutase-1
KeywordsISOMERASE / phosphoglucomutase / enzyme / missense variant
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-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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III ...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, 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
Similarity search - Domain/homology
Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsStiers, K.M. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateTRIUMPH Award United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Effects of the T337M and G391V disease-related variants on human phosphoglucomutase 1: structural disruptions large and small.
Authors: Stiers, K.M. / Owuocha, L.F. / Beamer, L.J.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,5643
Polymers128,4682
Non-polymers961
Water55831
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3302
Polymers64,2341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglucomutase-1


Theoretical massNumber of molelcules
Total (without water)64,2341
Polymers64,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.050, 171.050, 100.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 64233.812 Da / Num. of mol.: 2 / Mutation: G391V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: condition 2-33 of the Morpheus crystal screen (Molecular Dimensions) at a protein concentration of 10 mg/mL from a hanging drop of 1 ml protein and 4 ml well buffer. Condition 2-33 contains ...Details: condition 2-33 of the Morpheus crystal screen (Molecular Dimensions) at a protein concentration of 10 mg/mL from a hanging drop of 1 ml protein and 4 ml well buffer. Condition 2-33 contains 0.1 M of a carboxylic acid mixture (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M sodium potassium tartrate tetrahydrate, and 0.2 M sodium oxamate), 0.1 M of a buffer system at pH 8.5 (Tris base and BICINE), and a 30% v/v precipitant mix (40% v/v PEG 500 MME and 20% w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000001 Å / Relative weight: 1
ReflectionResolution: 2.8→48.18 Å / Num. obs: 37211 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 76.01 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.04536 / Rrim(I) all: 0.16 / Net I/σ(I): 15.44
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.24 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 3643 / CC1/2: 0.512 / CC star: 0.823 / Rpim(I) all: 0.8299 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5epc

5epc


Resolution: 2.8→48.18 Å / SU ML: 0.4211 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4841 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2518 1862 5 %
Rwork0.1927 35342 -
obs0.1956 37204 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7874 0 5 31 7910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00958025
X-RAY DIFFRACTIONf_angle_d1.09510914
X-RAY DIFFRACTIONf_chiral_restr0.0631278
X-RAY DIFFRACTIONf_plane_restr0.00631422
X-RAY DIFFRACTIONf_dihedral_angle_d4.65286348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.40981400.32772675X-RAY DIFFRACTION99.96
2.88-2.960.33711400.28752675X-RAY DIFFRACTION99.96
2.96-3.060.36851410.26562665X-RAY DIFFRACTION100
3.06-3.170.31081410.24242678X-RAY DIFFRACTION99.96
3.17-3.290.33491410.24172677X-RAY DIFFRACTION100
3.29-3.440.3161410.21952688X-RAY DIFFRACTION100
3.44-3.620.33221420.20062693X-RAY DIFFRACTION100
3.62-3.850.26291430.18592705X-RAY DIFFRACTION100
3.85-4.150.24791430.1722717X-RAY DIFFRACTION100
4.15-4.560.19311430.15122722X-RAY DIFFRACTION100
4.56-5.220.18771450.14742744X-RAY DIFFRACTION100
5.22-6.580.22831470.20592783X-RAY DIFFRACTION100
6.58-48.180.23021550.1832920X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.72020091026-0.978189349464-0.6432266001614.229716512430.2665078771381.81193511566-0.0939096211837-0.250552315907-0.06605090858150.5741154206870.348747384006-0.4275814655680.4366189088650.472902752547-0.2218421831320.5962618392230.068186189499-0.1295972941160.515730362026-0.1200880002020.4699827958233.5777401685-71.14764736651.49250501391
21.20035091975-0.942851744057-0.6987785768923.119823797542.058666106692.290263372760.09152798895330.214312515560.21621155013-0.3305191873280.425626387055-1.02556093505-0.4096824952510.636750310526-0.3130807183880.467387704064-0.1578894861130.1188695340420.535739798876-0.07594455603340.76691303002431.4893639303-40.8607502929-3.06255688279
32.620956759921.519023461611.306166611972.072332056560.7626798618294.191789188010.118226505865-0.443079667838-0.001538875088970.155984978062-0.239708957694-0.00372526451530.0247243959761-0.3616177875910.1000393925410.306932767844-0.007841092850080.01210625481680.45017074783-0.03164710489620.47651471536918.9226302367-42.971874137616.9212897572
42.881779567761.164434852320.1645565924412.747302162460.4111261938143.17735283761-0.01575030148770.3911662943210.181442499865-0.3130965676130.2970080269770.4799488467230.295993175732-0.732350889852-0.2172793489620.442267768770.00608519493459-0.07819458840220.7725987832980.1633922855470.555816933048-25.4611355088-56.7982634013-9.14585372367
52.06042015739-0.332025338786-1.02723062313.313293010770.1337921136922.703352585870.2761160146630.6559568948820.132787863767-1.19799975828-0.2305858211740.332816340014-0.553000897069-0.270138722991-0.06872096545760.7884018062050.156646553568-0.1272650665530.770850795029-0.01708289598750.523342052511-6.93927739594-38.267259573-23.1753437662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 319 )
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 247 )
5X-RAY DIFFRACTION5chain 'B' and (resid 248 through 562 )

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