1bhe

POLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA

Method: X-RAY DIFFRACTION D_max: 70.1 Å Quality: GOOD

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

POLYGALACTURONASE

Pectobacterium carotovorum subsp. carotovorum

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 27–402	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 0.1M SODIUM CACODYLATE, PH 6.5, 0.2M MAGNESIUM ACETATE.	Resolution 1.90 Å R-free 0.239

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PGLR2_ERWCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–376； UniProt 27–402

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	1bhe
Deposition date deposition_date	1998-06-05
Structure title title	POLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA
Keywords keywords	FAMILY 28 GLYCOSYL HYDROLASE, HYDROLYSES POLYGALACTURONIC ACID, GLYCOSIDASE; GLYCOSIDASE
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	21.58 Å
Radius of gyration Rg (electron density) rg_electron	20.76 Å
Forward intensity I(0) i0	28191600.00
Molecular weight molecular_weight	40099.0 kDa
Excluded volume excluded_volume	50029 Å³
Envelope volume envelope_volume	58199 Å³
Hydration-shell volume shell_volume	23182 Å³
Envelope diameter envelope_diameter	70.1 Å
Shell Rg shell_rg	27.53 Å
Envelope Rg envelope_rg	21.12 Å
Shape Rg shape_rg	20.71 Å
Total Rg total_rg	21.74 Å
Total atoms total_atoms	2813
Residues n_residues	376
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	70.1 Å
Rg (real space) rg_real	21.51 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.8190e+07
I(0) uncertainty (real space) i0_real_error	3.7740e+05
Rg (reciprocal space) rg_reciprocal	21.52 Å
I(0) (reciprocal space) i0_reciprocal	28190000.0000
Solution quality estimate total_estimate	0.8890
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3481000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bhea_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

CATH v4.4 (1 domains)

Domain ID domain_id	1bheA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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8. Citations (1)

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Unit-cell length a length_a	81.229 Å
Unit-cell length b length_b	53.033 Å
Unit-cell length c length_c	103.093 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	12.500 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2390

Description description	POLYGALACTURONASE
Molecular weight formula_weight	40135.2 kDa
EC 编号 ec_number	3.2.1.15
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3108

POLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA

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

POLYGALACTURONASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pectobacterium carotovorum subsp. carotovorum
NCBI Class编号 ncbi_taxonomy_id	555
宿主生物 host_organism	Bacillus subtilis

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

fit	/app/data/saxs_computation/bh/1bhe/1bhe.fit
pddf	/app/data/pr_computation/bh/1bhe/1bhe.pr.out
profile	/app/data/saxs_computation/bh/1bhe/1bhe.dat