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3pmg

STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY

Method: X-RAY DIFFRACTION Dmax: 133.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphoglucomutase-1

OrganismNot specified

UniProt P00949

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–561 Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.191
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–561 Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.191

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 3PMG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C47 BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTASE ASSOCIATED WITH CHEMICAL REACTION Deposited 1999-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–562（561 aa）
Chain B 2–562（561 aa）
Not recorded G16 1,6-di-O-phosphono-alpha-D-glucopyranose × 1 CD CADMIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.248
1C4G PHOSPHOGLUCOMUTASE VANADATE BASED TRANSITION STATE ANALOG COMPLEX Deposited 1999-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–562（561 aa）
Chain B 2–562（561 aa）
Not recorded CO COBALT (II) ION × 1 VG1 ALPHA-D-GLUCOSE-1-PHOSPHATE-6-VANADATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.290
1JDY RABBIT MUSCLE PHOSPHOGLUCOMUTASE Deposited 1996-07-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–561（561 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CD CADMIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；pH 6.4
Resolution 2.70 Å R-free 0.244
1JDY RABBIT MUSCLE PHOSPHOGLUCOMUTASE Deposited 1996-07-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–561（561 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CD CADMIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；pH 6.4
Resolution 2.70 Å R-free 0.244
1LXT STRUCTURE OF PHOSPHOTRANSFERASE PHOSPHOGLUCOMUTASE FROM RABBIT Deposited 1996-07-28 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–561（561 aa）
Not recorded CD CADMIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.260
1LXT STRUCTURE OF PHOSPHOTRANSFERASE PHOSPHOGLUCOMUTASE FROM RABBIT Deposited 1996-07-28 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–561（561 aa）
Not recorded CD CADMIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.260
1VKL RABBIT MUSCLE PHOSPHOGLUCOMUTASE Deposited 1996-07-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–561（561 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；pH 6.4
Resolution 2.70 Å R-free 0.210
1VKL RABBIT MUSCLE PHOSPHOGLUCOMUTASE Deposited 1996-07-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–561（561 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；pH 6.4
Resolution 2.70 Å R-free 0.210

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PGMU_RABIT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–561； UniProt 1–561 Author chain B； PDBConstruct 1–561； UniProt 1–561

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 3pmg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3pmg
Deposition date deposition_date1995-03-02
Structure title titleSTRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY
Keywords keywordsPHOSPHOTRANSFERASE, 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_guinier37.10 Å
Radius of gyration Rg (electron density) rg_electron36.99 Å
Forward intensity I(0) i0226399000.00
Molecular weight molecular_weight123060.0 kDa
Excluded volume excluded_volume154650 ų
Envelope volume envelope_volume193050 ų
Hydration-shell volume shell_volume44703 ų
Envelope diameter envelope_diameter140.9 Å
Shell Rg shell_rg41.33 Å
Envelope Rg envelope_rg37.07 Å
Shape Rg shape_rg37.00 Å
Total Rg total_rg37.24 Å
Total atoms total_atoms10610
Residues n_residues1120
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 dmax133.6 Å
Rg (real space) rg_real37.43 Å
Rg uncertainty (real space) rg_real_error1.94 Å
I(0) (real space) i0_real2.2640e+08
I(0) uncertainty (real space) i0_real_error4.6390e+06
Rg (reciprocal space) rg_reciprocal37.23 Å
I(0) (reciprocal space) i0_reciprocal226400000.0000
Solution quality estimate total_estimate0.8147
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.2 Å
Skewness Skewness skewness0.573
Kurtosis Kurtosis kurtosis-0.126
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60910000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.696; Smooth: 0.885
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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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3pmga1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmga2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmga3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmga4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.2 — Phosphoglucomutase, C-terminal domain
Family Family familyd.129.2.1 — Phosphoglucomutase, C-terminal domain
Domain ID domain_idd3pmgb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmgb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmgb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamilyc.84.1 — Phosphoglucomutase, first 3 domains
Family Family familyc.84.1.1 — Phosphoglucomutase, first 3 domains
Domain ID domain_idd3pmgb4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.2 — Phosphoglucomutase, C-terminal domain
Family Family familyd.129.2.1 — Phosphoglucomutase, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id3pmgA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily50 — Alpha-D-phosphohexomutase, C-terminal domain
Domain ID domain_id3pmgB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Domain ID domain_id3pmgB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily50 — Alpha-D-phosphohexomutase, C-terminal domain
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8. Citations (5)

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9. Files and Curves (10)