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- PDB-6snq: Crystal structures of human PGM1 isoform 2 -

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Basic information

Entry
Database: PDB / ID: 6snq
TitleCrystal structures of human PGM1 isoform 2
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / Phosphoglucomutase / hexose metabolism
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
6-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBacke, P.H. / Laerdahl, J.K. / Kittelsen, L.S. / Dalhus, B. / Morkrid, L. / Bjoras, M.
CitationJournal: Sci Rep / Year: 2020
Title: Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the alpha-D-phosphohexomutase superfamily.
Authors: Backe, P.H. / Laerdahl, J.K. / Kittelsen, L.S. / Dalhus, B. / Morkrid, L. / Bjoras, M.
History
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4523
Polymers64,1261
Non-polymers3262
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-2 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.262, 53.155, 76.825
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 64126.496 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: KCl, MgCl2, Na cacodylate pH 6.5 and PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→48.63 Å / Num. obs: 16247 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.043 / Rrim(I) all: 0.092 / Net I/σ(I): 13.1
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 2160 / CC1/2: 0.925 / Rpim(I) all: 0.286 / Rrim(I) all: 0.632

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.63 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.66
RfactorNum. reflection% reflection
Rfree0.2461 804 4.96 %
Rwork0.2059 --
obs0.2079 16195 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 17 84 4502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024511
X-RAY DIFFRACTIONf_angle_d0.4816101
X-RAY DIFFRACTIONf_dihedral_angle_d2.5042685
X-RAY DIFFRACTIONf_chiral_restr0.042671
X-RAY DIFFRACTIONf_plane_restr0.003790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86930.38711580.32122486X-RAY DIFFRACTION98
2.8693-3.09080.31281300.26962564X-RAY DIFFRACTION100
3.0908-3.40170.33291250.22552530X-RAY DIFFRACTION99
3.4017-3.89380.25461180.20222602X-RAY DIFFRACTION100
3.8938-4.9050.19681250.16582584X-RAY DIFFRACTION100
4.905-48.63760.19131480.18892625X-RAY DIFFRACTION99

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