1c47

BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTASE ASSOCIATED WITH CHEMICAL REACTION

Method: X-RAY DIFFRACTION D_max: 131.4 Å Quality: GOOD

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

ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–562 Chain B； UniProt 2–562	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 experimental conditions	Resolution 2.70 Å R-free 0.248

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 1C47	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4G PHOSPHOGLUCOMUTASE VANADATE BASED TRANSITION STATE ANALOG COMPLEX Deposited 1999-08-24	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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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
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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 9 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 2–562 Author chain B； PDBConstruct 1–561； UniProt 2–562

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	1c47
Deposition date deposition_date	1999-08-11
Structure title title	BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTASE ASSOCIATED WITH CHEMICAL REACTION
Keywords keywords	PHOSPHOGLUCOMUTASE, PHOSPHOTRANSFERASE WITH BOUND REACTION INTERMEDIATE, TRANSFERASE; TRANSFERASE
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	36.99 Å
Radius of gyration Rg (electron density) rg_electron	36.89 Å
Forward intensity I(0) i0	229293000.00
Molecular weight molecular_weight	123410.0 kDa
Excluded volume excluded_volume	154890 Å³
Envelope volume envelope_volume	193860 Å³
Hydration-shell volume shell_volume	44932 Å³
Envelope diameter envelope_diameter	140.2 Å
Shell Rg shell_rg	41.24 Å
Envelope Rg envelope_rg	37.03 Å
Shape Rg shape_rg	36.91 Å
Total Rg total_rg	37.12 Å
Total atoms total_atoms	8680
Residues n_residues	1122
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	131.4 Å
Rg (real space) rg_real	37.31 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	2.2930e+08
I(0) uncertainty (real space) i0_real_error	3.8540e+06
Rg (reciprocal space) rg_reciprocal	37.11 Å
I(0) (reciprocal space) i0_reciprocal	229200000.0000
Solution quality estimate total_estimate	0.8176
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.6 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	69890000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.721; Smooth: 0.825

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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	ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE
Molecular weight formula_weight	61499.9 kDa
EC 编号 ec_number	2.7.5.1
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	8828

VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT

Entity 2 Entity 2 non-polymer

Description description	1,6-di-O-phosphono-alpha-D-glucopyranose
Molecular weight formula_weight	339.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 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	148

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1c47a1
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	d1c47a2
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	d1c47a3
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	d1c47a4
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	d1c47b1
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	d1c47b2
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	d1c47b3
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	d1c47b4
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	1c47A01
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	1c47A02
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	1c47A03
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	1c47A04
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	1c47B01
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	1c47B02
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	1c47B03
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	1c47B04
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 (7)

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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	101.100 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	0.1830
R_work r_work	0.1830
R_free r_free	0.2480

fit	/app/data/saxs_computation/c4/1c47/1c47.fit
pddf	/app/data/pr_computation/c4/1c47/1c47.pr.out
profile	/app/data/saxs_computation/c4/1c47/1c47.dat