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- PDB-1gzv: The crystal structure of phosphoglucose isomerase from pig muscle... -

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Basic information

Entry
Database: PDB / ID: 1gzv
TitleThe crystal structure of phosphoglucose isomerase from pig muscle complexed with 5-phosphoarabinonate
ComponentsGLUCOSE-6-PHOSPHATE ISOMERASE
KeywordsISOMERASE / ALDOSE-KETOSE ISOMERASE / 5-PHOSPHOARABINONATE / GLYCOLYTIC ENZYME / CYTOKINE
Function / homology
Function and homology information


Glycolysis / TP53 Regulates Metabolic Genes / Gluconeogenesis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / Neutrophil degranulation / carbohydrate derivative binding / monosaccharide binding / fructose 6-phosphate metabolic process ...Glycolysis / TP53 Regulates Metabolic Genes / Gluconeogenesis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / Neutrophil degranulation / carbohydrate derivative binding / monosaccharide binding / fructose 6-phosphate metabolic process / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / mesoderm formation / positive regulation of endothelial cell migration / cytokine activity / gluconeogenesis / glycolytic process / glucose homeostasis / in utero embryonic development / ubiquitin protein ligase binding / extracellular space / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 3.51 Å
AuthorsDavies, C. / Muirhead, H.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 2002
Title: Crystal Structure of Phosphoglucose Isomerase from Pig Muscle and its Complex with 5-Phosphoarabinonate
Authors: Davies, C. / Muirhead, H.
#1: Journal: J.Mol.Biol. / Year: 1977
Title: Crystallographic Structure Analysis of Glucose 6-Phosphate Isomerase at 3.5A Resolution
Authors: Shaw, P.J. / Muirhead, H.
#2: Journal: FEBS Lett. / Year: 1976
Title: The Active Site of Glucose Phosphate Isomerase
Authors: Shaw, P.J. / Muirhead, H.
History
DepositionJun 6, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE-6-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3242
Polymers63,0781
Non-polymers2461
Water00
1
A: GLUCOSE-6-PHOSPHATE ISOMERASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6484
Polymers126,1552
Non-polymers4922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)95.600, 95.600, 138.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GLUCOSE-6-PHOSPHATE ISOMERASE / GPI / PHOSPHOGLUCOSE ISOMERASE / PGI / PHOSPHOHEXOSE ISOMERASE / PHI


Mass: 63077.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Tissue: MUSCLE / References: UniProt: P08059, glucose-6-phosphate isomerase
#2: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O9P
Compound detailsCONVERTS D-GLUCOSE 6-PHOSPHATE = D-FRUCTOSE 6- PHOSPHATE AND IS INVOLVED IN GLYCOLYSIS AND IN GLUCONEOGENESIS.
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 277 K / pH: 7
Details: THE PROTEIN WAS CONCENTRATED TO 10MG/ML AND CRYSTALLIZED AT 4 DEGRESS CELSIUS FROM 10MM SODIUM PHOSPHATE, PH 7.5 AND 57% SATURATED AMMONIUM SULPHATE.

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOT / Wavelength: 1.5418
DetectorType: HILGER-WATTS / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→17.7 Å / Num. obs: 7817 / % possible obs: 92.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.045

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Processing

SoftwareName: REFMAC / Version: 5.0.32 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 3.51→15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.866 / SU B: 31.5 / SU ML: 0.514 / Cross valid method: THROUGHOUT / ESU R Free: 0.687 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 358 4.6 %RANDOM
Rwork0.19 ---
obs-7414 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 42.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å20 Å2
2---2.47 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 3.51→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 15 0 4437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9356156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2233553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.32098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.380
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.611.52752
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23224439
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95131795
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5734.51717
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.51→3.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 29
Rwork0.214 519

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