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- PDB-5tr2: Crystal structure of the D263G missense variant of human PGM1 -

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Basic information

Entry
Database: PDB / ID: 5tr2
TitleCrystal structure of the D263G 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, C-terminal domain / 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 / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBeamer, L.J. / Stiers, K.M.
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
DepositionOct 25, 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 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)128,9849
Polymers128,4272
Non-polymers5577
Water3,675204
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6346
Polymers64,2141
Non-polymers4205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3503
Polymers64,2141
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.124, 172.124, 99.005
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
11B-778-

HOH

21B-779-

HOH

DetailsMonomer according to Dynamic Light Scattering and Literature

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Components

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


Mass: 64213.680 Da / Num. of mol.: 2 / Mutation: D263G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli)
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.: 4 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.85 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Ammonium Sulfate, 0.1 M NaCl, and 0.1 M HEPES pH 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 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.5→57.37 Å / Num. obs: 44375 / % possible obs: 85.4 % / Redundancy: 14 % / CC1/2: 0.998 / Rmerge(I) obs: 0.194 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.027 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.592 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSVERSION May 1, 2016 BUILT=20160517data reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.5→51.844 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.2919 2208 5.01 %
Rwork0.22 --
obs0.2236 44106 85.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7913 0 28 204 8145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018193
X-RAY DIFFRACTIONf_angle_d1.06611188
X-RAY DIFFRACTIONf_dihedral_angle_d14.9914817
X-RAY DIFFRACTIONf_chiral_restr0.0641267
X-RAY DIFFRACTIONf_plane_restr0.0071496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55440.38021880.30513001X-RAY DIFFRACTION100
2.5544-2.61380.37021630.29553044X-RAY DIFFRACTION100
2.6138-2.67910.44371470.34493025X-RAY DIFFRACTION100
2.6791-2.75160.35061690.30123031X-RAY DIFFRACTION100
2.7516-2.83250.36841690.26393029X-RAY DIFFRACTION100
2.8325-2.9240.33291690.26993036X-RAY DIFFRACTION100
2.924-3.02840.3031420.23273052X-RAY DIFFRACTION100
3.0284-3.14970.32851470.22713065X-RAY DIFFRACTION100
3.1497-3.2930.29331400.22173052X-RAY DIFFRACTION99
3.293-3.46660.3265690.24621543X-RAY DIFFRACTION90
3.6837-3.96810.3345200.1885354X-RAY DIFFRACTION96
3.9681-4.36720.26191720.17773082X-RAY DIFFRACTION100
4.3672-4.99870.24241810.16543094X-RAY DIFFRACTION100
4.9987-6.29610.25631680.21153162X-RAY DIFFRACTION100
6.2961-51.85540.25621640.19913328X-RAY DIFFRACTION100
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)
10.15630.03230.04420.2905-0.06720.13360.0939-0.17410.06640.04090.09540.0264-0.08050.57680.28060.2296-0.05530.06810.4788-0.16540.315771.587734.7319-22.3558
20.0987-0.0127-0.09740.0299-0.00970.17140.08730.19090.162-0.0895-0.04710.04570.0462-0.04770.00010.21570.04520.03530.19970.01090.324944.489130.6156-29.153
30.1969-0.1181-0.1970.3513-0.08990.2154-0.0685-0.0160.04890.14580.03720.02430.29740.1087-0.00020.2690.04220.01470.1812-0.04470.24143.345119.1055-8.1033
40.3322-0.2294-0.19760.45290.12160.10560.2932-0.20880.05820.6094-0.0757-0.37860.3075-0.57490.27550.5866-0.1392-0.0950.41130.11670.188822.980357.8296-35.9881
50.1397-0.11520.08750.20050.11470.43490.27490.1413-0.420.19390.425-0.42820.34550.18820.82740.19580.0946-0.1412-0.316-0.57510.101845.985265.0805-44.3457
60.6496-0.0798-0.13410.04010.0750.13240.29150.09730.04570.53450.0131-0.1534-0.04240.00070.12110.7281-0.087-0.06640.2545-0.02720.358744.885880.4782-26.016
70.00250.00090.0101-0.0025-0.00160.00740.0068-0.1754-0.03830.21520.1161-0.01020.0390.2022-00.84640.0106-0.19130.5788-0.0460.485654.731775.0682-14.4806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 319 )
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 183 )
5X-RAY DIFFRACTION5chain 'B' and (resid 184 through 293 )
6X-RAY DIFFRACTION6chain 'B' and (resid 294 through 512 )
7X-RAY DIFFRACTION7chain 'B' and (resid 513 through 562 )

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