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- PDB-2pgi: THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE-AN ENZYME WITH ... -

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Basic information

Entry
Database: PDB / ID: 2pgi
TitleTHE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE-AN ENZYME WITH AUTOCRINE MOTILITY FACTOR ACTIVITY IN TUMOR CELLS
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / PHOSPHOGLUCOSE ISOMERASE / AUTOCRINEFACTOR / NEUROLEUKIN / MOTILITY / GLYCOLYSIS
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase 2
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsSun, Y.-J. / Chou, C.-C. / Chen, W.-S. / Meng, M. / Hsiao, C.-D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin.
Authors: Sun, Y.J. / Chou, C.C. / Chen, W.S. / Wu, R.T. / Meng, M. / Hsiao, C.D.
#1: Journal: J.Mol.Biol. / Year: 1977
Title: Crystallographic Structure Analysis of Glucose 6-Phosphate Isomerase at 3.5 A Resolution
Authors: Shaw, P.J. / Muirhead, H.
History
DepositionOct 27, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOGLUCOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)50,2031
Polymers50,2031
Non-polymers00
Water3,315184
1
A: PHOSPHOGLUCOSE ISOMERASE

A: PHOSPHOGLUCOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)100,4062
Polymers100,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area10880 Å2
ΔGint-71 kcal/mol
Surface area28900 Å2
MethodPISA
2
A: PHOSPHOGLUCOSE ISOMERASE

A: PHOSPHOGLUCOSE ISOMERASE

A: PHOSPHOGLUCOSE ISOMERASE

A: PHOSPHOGLUCOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)200,8114
Polymers200,8114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area26200 Å2
ΔGint-158 kcal/mol
Surface area53340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.100, 93.730, 171.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE / GLUCOSE-6-PHOSPHATE ISOMERASE


Mass: 50202.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: PGIB / Plasmid: PMMB67EH / Production host: Escherichia coli (E. coli) / Strain (production host): DF2145 / References: UniProt: P13376, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-ID
1mg/mlprotein1drop
2mM6-phosphogluconate1drop
3mMphosphate1drop
4mMphosphate1reservoir
5Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 25, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30.7 Å / Num. obs: 24024 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.11 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 83.4
Reflection
*PLUS
Num. measured all: 104060
Reflection shell
*PLUS
% possible obs: 83.4 % / Rmerge(I) obs: 0.362

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2319 8.7 %RANDOM
Rwork0.185 ---
obs0.185 23447 87.93 %-
Displacement parametersBiso mean: 21.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 184 3698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 260 7.8 %
Rwork0.269 2286 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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