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- PDB-1u0f: Crystal structure of mouse phosphoglucose isomerase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1u0f
TitleCrystal structure of mouse phosphoglucose isomerase in complex with glucose 6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / aldose-ketose isomerase / dimer
Function / homology
Function and homology information


glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / canonical glycolysis ...glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / canonical glycolysis / erythrocyte homeostasis / ciliary membrane / response to testosterone / positive regulation of immunoglobulin production / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / Neutrophil degranulation / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / glycolytic process / growth factor activity / glucose homeostasis / response to estradiol / myelin sheath / negative regulation of neuron apoptotic process / in utero embryonic development / learning or memory / ubiquitin protein ligase binding / extracellular space / plasma membrane / 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
BETA-MERCAPTOETHANOL / 6-O-phosphono-alpha-D-glucopyranose / GLUCOSE-6-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT FROM THE NATIVE STRUCTURE / Resolution: 1.6 Å
AuthorsSolomons, J.T.G. / Zimmerly, E.M. / Burns, S. / Krishnamurthy, N. / Swan, M.K. / Krings, S. / Muirhead, H. / Chirgwin, J. / Davies, C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The crystal structure of mouse phosphoglucose isomerase at 1.6A resolution and its complex with glucose 6-phosphate reveals the catalytic mechanism of sugar ring opening.
Authors: Graham Solomons, J.T. / Zimmerly, E.M. / Burns, S. / Krishnamurthy, N. / Swan, M.K. / Krings, S. / Muirhead, H. / Chirgwin, J. / Davies, C.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE RESIDUE 263 IS A LEU NOT A PHE AS SHOWN BY THE SEQUENCE OF THE CONSTRUCT AS WELL AS THE ...SEQUENCE RESIDUE 263 IS A LEU NOT A PHE AS SHOWN BY THE SEQUENCE OF THE CONSTRUCT AS WELL AS THE ELECTRON DENSITY MAP. IT APPEARS TO EMANATE FROM THE ORIGINAL EXPRESSED SEQUENCE TAG AND IS NOT A PCR ERROR. HENCE THIS IS A POLYMORPHISM IN THE MAMMARY CELL LINE USED TO MAKE THE CDNA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,76125
Polymers127,2892
Non-polymers2,47223
Water15,457858
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18600 Å2
ΔGint-195 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.400, 116.800, 73.900
Angle α, β, γ (deg.)90.00, 101.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. The asymmetric unit is a dimer

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Glucose-6-phosphate isomerase / / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI / Neuroleukin / NLK


Mass: 63644.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpi / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3pLysS / References: UniProt: P06745, glucose-6-phosphate isomerase
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 880 molecules

#3: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE / Glucose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.3 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.9 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45 Å / Num. all: 143578 / Num. obs: 143578 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 34.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.1 / Num. unique all: 12096 / Rsym value: 0.369 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: REFINEMENT FROM THE NATIVE STRUCTURE
Starting model: NATIVE STRUCTURE

Resolution: 1.6→45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.787 / SU ML: 0.062 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.207 7210 5 %RANDOM
Rwork0.178 ---
all0.18 143578 --
obs0.18 143578 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å21.09 Å2
2---1.55 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8814 0 148 858 9820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.95212487
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57851110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.24340
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5951.55534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09528946
X-RAY DIFFRACTIONr_scbond_it1.77933705
X-RAY DIFFRACTIONr_scangle_it2.9174.53541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.252 437
Rwork0.232 8373
obs-8810

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