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2pgi

THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE-AN ENZYME WITH AUTOCRINE MOTILITY FACTOR ACTIVITY IN TUMOR CELLS

Method: X-RAY DIFFRACTION Dmax: 79.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHOGLUCOSE ISOMERASE

Geobacillus stearothermophilus

UniProt P13376

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–445 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0 Resolution 2.30 Å R-free 0.278
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–445 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0 Resolution 2.30 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2PGI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B0Z The crystal structure of phosphoglucose isomerase-an enzyme with autocrine motility factor activity in tumor cells Deposited 1998-11-15 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–445（445 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION FROM 4-UL DROPLETS OF PROTEIN SOLUTION (15 MG/ML) IN 50 MM PHOSPHATE BUFFER (PH7.0) AND 0.2 M AMMONIUM PHOSPHATE AGAINST A RESERVOIR OF THE ABOVE BUFFER CONTAINING 0.4M AMMONIUM PHOSPHATE., VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.258
1B0Z The crystal structure of phosphoglucose isomerase-an enzyme with autocrine motility factor activity in tumor cells Deposited 1998-11-15 Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–445（445 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION FROM 4-UL DROPLETS OF PROTEIN SOLUTION (15 MG/ML) IN 50 MM PHOSPHATE BUFFER (PH7.0) AND 0.2 M AMMONIUM PHOSPHATE AGAINST A RESERVOIR OF THE ABOVE BUFFER CONTAINING 0.4M AMMONIUM PHOSPHATE., VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.258
1C7Q THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTILITY FACTOR/NEUROLEUKIN COMPLEXED WITH ITS CARBOHYDRATE PHOSPHATE INHIBITORS AND ITS SUBSTRATE RECOGNITION MECHANISM Deposited 2000-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–445（445 aa）
Not recorded BE1 N-BROMOACETYL-AMINOETHYL PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 0.8M K, NA TARTRATE
Resolution 2.30 Å R-free 0.242
1C7R THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTILITY FACTOR/NEUROLEUKIN COMPLEXED WITH ITS CARBOHYDRATE PHOSPHATE INHIBITORS AND ITS SUBSTRATE RECOGNITION MECHANISM Deposited 2000-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–445（445 aa）
Not recorded PA5 5-PHOSPHOARABINONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.5, 0.8M K, NA TARTRATE
Resolution 2.50 Å R-free 0.289
1C7R THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTILITY FACTOR/NEUROLEUKIN COMPLEXED WITH ITS CARBOHYDRATE PHOSPHATE INHIBITORS AND ITS SUBSTRATE RECOGNITION MECHANISM Deposited 2000-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–445（445 aa）
Not recorded PA5 5-PHOSPHOARABINONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.5, 0.8M K, NA TARTRATE
Resolution 2.50 Å R-free 0.289

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G6PIB_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–445； UniProt 1–445

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2pgi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2pgi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2pgi
Deposition date deposition_date1998-10-27
Structure title titleTHE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE-AN ENZYME WITH AUTOCRINE MOTILITY FACTOR ACTIVITY IN TUMOR CELLS
Keywords keywordsPHOSPHOGLUCOSE ISOMERASE, AUTOCRINEFACTOR, NEUROLEUKIN, MOTILITY, GLYCOLYSIS, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.59 Å
Radius of gyration Rg (electron density) rg_electron23.43 Å
Forward intensity I(0) i040308700.00
Molecular weight molecular_weight49766.0 kDa
Excluded volume excluded_volume62496 ų
Envelope volume envelope_volume75591 ų
Hydration-shell volume shell_volume26877 ų
Envelope diameter envelope_diameter83.1 Å
Shell Rg shell_rg30.66 Å
Envelope Rg envelope_rg23.79 Å
Shape Rg shape_rg23.41 Å
Total Rg total_rg24.33 Å
Total atoms total_atoms3514
Residues n_residues442
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.7 Å
Rg (real space) rg_real24.50 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real4.0310e+07
I(0) uncertainty (real space) i0_real_error4.3530e+05
Rg (reciprocal space) rg_reciprocal24.52 Å
I(0) (reciprocal space) i0_reciprocal40310000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5932000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2pgia_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.80 — SIS domain
Superfamily Superfamily superfamilyc.80.1 — SIS domain
Family Family familyc.80.1.2 — Phosphoglucose isomerase, PGI

CATH v4.4 (2 domains)

Domain ID domain_id2pgiA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10490 — Glucose-6-phosphate isomerase like protein; domain 1
Domain ID domain_id2pgiA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10490 — Glucose-6-phosphate isomerase like protein; domain 1
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8. Citations (2)

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9. Files and Curves (10)