5pgm

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE

Method: X-RAY DIFFRACTION D_max: 167.6 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHOGLYCERATE MUTASE 1

OrganismNot specified

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 1–246 Chain B； UniProt 1–246 Chain C； UniProt 1–246 Chain D； UniProt 1–246	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–246 Chain F； UniProt 1–246 Chain G； UniProt 1–246 Chain H； UniProt 1–246	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

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 5PGM	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 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 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–240（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
3PGM THE STRUCTURE OF YEAST PHOSPHOGLYCERATE MUTASE AT 0.28 NM RESOLUTION Deposited 1982-04-06	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 1–235（235 aa） Chain B 1–235（235 aa）	Not recorded	SO4 SULFATE ION × 8 3PG 3-PHOSPHOGLYCERIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
4PGM SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE Deposited 1997-04-25	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

5 other PDB entries and 5 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 1–246； UniProt 1–246 Author chain B； PDBConstruct 1–246； UniProt 1–246 Author chain C； PDBConstruct 1–246； UniProt 1–246 Author chain D； PDBConstruct 1–246； UniProt 1–246 Author chain E； PDBConstruct 1–246； UniProt 1–246 Author chain F； PDBConstruct 1–246； UniProt 1–246 Author chain G； PDBConstruct 1–246； UniProt 1–246 Author chain H； PDBConstruct 1–246； UniProt 1–246

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5pgm
Deposition date deposition_date	1998-08-19
Structure title title	SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE
Keywords keywords	ISOMERASE, TRANSFERASE (PHOSPHORYL), GLYCOLYTIC ENZYME; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	48.04 Å
Radius of gyration Rg (electron density) rg_electron	48.25 Å
Forward intensity I(0) i0	633237000.00
Molecular weight molecular_weight	213120.0 kDa
Excluded volume excluded_volume	268710 Å³
Envelope volume envelope_volume	358770 Å³
Hydration-shell volume shell_volume	64055 Å³
Envelope diameter envelope_diameter	178.8 Å
Shell Rg shell_rg	50.10 Å
Envelope Rg envelope_rg	47.50 Å
Shape Rg shape_rg	48.24 Å
Total Rg total_rg	48.34 Å
Total atoms total_atoms	15054
Residues n_residues	1877
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	167.6 Å
Rg (real space) rg_real	48.51 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	6.3340e+08
I(0) uncertainty (real space) i0_real_error	1.1320e+07
Rg (reciprocal space) rg_reciprocal	48.04 Å
I(0) (reciprocal space) i0_reciprocal	632900000.0000
Solution quality estimate total_estimate	0.6101
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.7 Å
Skewness Skewness skewness	0.455
Kurtosis Kurtosis kurtosis	-0.516
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0209
Highest regularization parameter α highest_alpha	42220000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.894

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PHOSPHOGLYCERATE MUTASE 1
Molecular weight formula_weight	27517.4 kDa
EC 编号 ec_number	5.4.2.1
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C,A,B,E,F,G,H
Atom count atom_count	16692

PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAVANQGKK

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1638

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5pgma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgme_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5pgmh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

CATH v4.4 (8 domains)

Domain ID domain_id	5pgmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5pgmH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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8. Citations (3)

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Unit-cell length a length_a	82.497 Å
Unit-cell length b length_b	93.262 Å
Unit-cell length c length_c	147.329 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2280

fit	/app/data/saxs_computation/pg/5pgm/5pgm.fit
pddf	/app/data/pr_computation/pg/5pgm/5pgm.pr.out
profile	/app/data/saxs_computation/pg/5pgm/5pgm.dat