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3pgm

THE STRUCTURE OF YEAST PHOSPHOGLYCERATE MUTASE AT 0.28 NM RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 87.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphoglycerate mutase 1

Saccharomyces cerevisiae

UniProt P00950

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–235 Chain B； UniProt 1–235 Not recorded SO4 SULFATE ION × 8 3PG 3-PHOSPHOGLYCERIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å

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 3PGM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BQ3 SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH INOSITOL HEXAKISPHOSPHATE Deposited 1998-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–247（246 aa）
Chain B 2–247（246 aa）
Chain C 2–247（246 aa）
Chain D 2–247（246 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.65；PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, pH 8.65
Resolution 2.70 Å R-free 0.240
1BQ4 SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH BENZENE HEXACARBOXYLATE Deposited 1998-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–247（246 aa）
Chain B 2–247（246 aa）
Chain C 2–247（246 aa）
Chain D 2–247（246 aa）
Not recorded SO4 SULFATE ION × 3 BHC BENZENE HEXACARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.65；PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, pH 8.65
Resolution 2.50 Å R-free 0.254
1QHF YEAST PHOSPHOGLYCERATE MUTASE-3PG COMPLEX STRUCTURE TO 1.7 A Deposited 1999-05-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–240（240 aa）
Chain B 1–240（240 aa）
Not recorded SO4 SULFATE ION × 8 3PG 3-PHOSPHOGLYCERIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；55% AMMONIUM SULFATE IN 10MM IMIDAZOLE BUFFER PH 6.8 WITH 1MM 3PG AND CONCENTRATION OF 10 MG ML PROTEIN
Resolution 1.70 Å R-free 0.215
4PGM SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE Deposited 1997-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Chain C 1–246（246 aa）
Chain D 1–246（246 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.65；PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, PH 8.65, 120MM LI2SO4, AND 1MM INOSITOL HEXAKISPHOSPHATE
Resolution 2.30 Å R-free 0.286
5PGM SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE Deposited 1998-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Chain C 1–246（246 aa）
Chain D 1–246（246 aa）
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.65；pH 8.65
Resolution 2.12 Å R-free 0.228
5PGM SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE Deposited 1998-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–246（246 aa）
Chain F 1–246（246 aa）
Chain G 1–246（246 aa）
Chain H 1–246（246 aa）
Not recorded SO4 SULFATE ION × 8 ALA ALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.65；pH 8.65
Resolution 2.12 Å R-free 0.228

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PMG1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–244； UniProt 1–235 Author chain B； PDBConstruct 1–244； UniProt 1–235

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 3pgm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3pgm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3pgm
Deposition date deposition_date1982-04-06
Structure title titleTHE STRUCTURE OF YEAST PHOSPHOGLYCERATE MUTASE AT 0.28 NM RESOLUTION
Keywords keywordsTRANSFERASE (PHOSPHORYL); TRANSFERASE (PHOSPHORYL)
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_guinier24.88 Å
Radius of gyration Rg (electron density) rg_electron24.19 Å
Forward intensity I(0) i045435900.00
Molecular weight molecular_weight52568.0 kDa
Excluded volume excluded_volume66040 ų
Envelope volume envelope_volume78111 ų
Hydration-shell volume shell_volume27199 ų
Envelope diameter envelope_diameter90.2 Å
Shell Rg shell_rg31.17 Å
Envelope Rg envelope_rg24.55 Å
Shape Rg shape_rg24.20 Å
Total Rg total_rg24.94 Å
Total atoms total_atoms3708
Residues n_residues460
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 dmax87.3 Å
Rg (real space) rg_real24.94 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real4.5440e+07
I(0) uncertainty (real space) i0_real_error7.0120e+05
Rg (reciprocal space) rg_reciprocal24.93 Å
I(0) (reciprocal space) i0_reciprocal45440000.0000
Solution quality estimate total_estimate0.8526
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.443
Kurtosis Kurtosis kurtosis-0.202
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12860000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.971
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3pgma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.1 — Cofactor-dependent phosphoglycerate mutase
Domain ID domain_idd3pgmb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.1 — Cofactor-dependent phosphoglycerate mutase

CATH v4.4 (2 domains)

Domain ID domain_id3pgmA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
Domain ID domain_id3pgmB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
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8. Citations (6)

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9. Files and Curves (10)