1jdy

RABBIT MUSCLE PHOSPHOGLUCOMUTASE

Method: X-RAY DIFFRACTION D_max: 130.5 Å Quality: GOOD

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

PHOSPHOGLUCOMUTASE

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 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)	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
2	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)	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

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 1JDY	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 experimental conditions 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 experimental conditions 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
1LXT STRUCTURE OF PHOSPHOTRANSFERASE PHOSPHOGLUCOMUTASE FROM RABBIT Deposited 1996-07-28	Different mutation/modification Different experimental conditions 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 experimental conditions 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 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 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
3PMG STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY Deposited 1995-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–561（561 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.191
3PMG STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY Deposited 1995-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–561（561 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.191

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

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	1jdy
Deposition date deposition_date	1996-07-11
Structure title title	RABBIT MUSCLE PHOSPHOGLUCOMUTASE
Keywords keywords	PHOSPHOGLUCOMUTASE, PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
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	37.03 Å
Radius of gyration Rg (electron density) rg_electron	36.96 Å
Forward intensity I(0) i0	230171000.00
Molecular weight molecular_weight	123430.0 kDa
Excluded volume excluded_volume	154810 Å³
Envelope volume envelope_volume	192580 Å³
Hydration-shell volume shell_volume	44669 Å³
Envelope diameter envelope_diameter	140.1 Å
Shell Rg shell_rg	41.16 Å
Envelope Rg envelope_rg	37.01 Å
Shape Rg shape_rg	36.98 Å
Total Rg total_rg	37.16 Å
Total atoms total_atoms	8678
Residues n_residues	1120
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	130.5 Å
Rg (real space) rg_real	37.36 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	2.3020e+08
I(0) uncertainty (real space) i0_real_error	3.8620e+06
Rg (reciprocal space) rg_reciprocal	37.16 Å
I(0) (reciprocal space) i0_reciprocal	230100000.0000
Solution quality estimate total_estimate	0.8146
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.571
Kurtosis Kurtosis kurtosis	-0.134
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	69840000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.739; Smooth: 0.719

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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	PHOSPHOGLUCOMUTASE
Molecular weight formula_weight	61579.9 kDa
EC 编号 ec_number	5.4.2.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9010

VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	332

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1jdya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdya3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdya4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.2 — Phosphoglucomutase, C-terminal domain
Family Family family	d.129.2.1 — Phosphoglucomutase, C-terminal domain

Domain ID domain_id	d1jdyb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdyb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdyb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.84 — Phosphoglucomutase, first 3 domains
Superfamily Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
Family Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

Domain ID domain_id	d1jdyb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.2 — Phosphoglucomutase, C-terminal domain
Family Family family	d.129.2.1 — Phosphoglucomutase, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1jdyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

Domain ID domain_id	1jdyB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

Domain ID domain_id	1jdyB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

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8. Citations (5)

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Unit-cell length a length_a	174.420 Å
Unit-cell length b length_b	174.420 Å
Unit-cell length c length_c	101.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2440

fit	/app/data/saxs_computation/jd/1jdy/1jdy.fit
pddf	/app/data/pr_computation/jd/1jdy/1jdy.pr.out
profile	/app/data/saxs_computation/jd/1jdy/1jdy.dat