SAXSdb — 1czf

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

POLYGALACTURONASE II

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 1–362	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG 4000, zinc sulphate, sodium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.68 Å R-free 0.191
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–362	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG 4000, zinc sulphate, sodium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.68 Å R-free 0.191
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–362 Chain B； UniProt 1–362	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG 4000, zinc sulphate, sodium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.68 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.

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

View Construct and Data Evidence

UniProt name	PGLR2_ASPNG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–362； UniProt 1–362 Author chain B； PDBConstruct 1–362； UniProt 1–362

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1czf
Deposition date deposition_date	1999-09-02
Structure title title	ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER
Keywords keywords	BETA HELIX, HYDROLASE; HYDROLASE
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	34.82 Å
Radius of gyration Rg (electron density) rg_electron	34.71 Å
Forward intensity I(0) i0	84932300.00
Molecular weight molecular_weight	70510.0 kDa
Excluded volume excluded_volume	86565 Å³
Envelope volume envelope_volume	107590 Å³
Hydration-shell volume shell_volume	26429 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	40.03 Å
Envelope Rg envelope_rg	34.14 Å
Shape Rg shape_rg	34.71 Å
Total Rg total_rg	35.07 Å
Total atoms total_atoms	4928
Residues n_residues	670
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	115.7 Å
Rg (real space) rg_real	35.07 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	8.4930e+07
I(0) uncertainty (real space) i0_real_error	1.4530e+06
Rg (reciprocal space) rg_reciprocal	34.92 Å
I(0) (reciprocal space) i0_reciprocal	84920000.0000
Solution quality estimate total_estimate	0.7893
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.848
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12170000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.573; Smooth: 0.898

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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	POLYGALACTURONASE II
Molecular weight formula_weight	37715.7 kDa
EC 编号 ec_number	3.2.1.15
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	5932

MHSFASLLAYGLVAGATFASASPIEARDSCTFTTAAAAKAGKAKCSTITLNNIEVPAGTTLDLTGLTSGTKVIFEGTTTFQYEEWAGPLISMSGEHITVTGASGHLINCDGARWWDGKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAFSVQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLESVTGSVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	980

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1czfa_
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

Domain ID domain_id	d1czfb_
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 (2 domains)

Domain ID domain_id	1czfA00
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

Domain ID domain_id	1czfB00
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	65.497 Å
Unit-cell length b length_b	201.241 Å
Unit-cell length c length_c	49.065 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1660
R_work r_work	0.1660
R_free r_free	0.1910

fit	/app/data/saxs_computation/cz/1czf/1czf.fit
pddf	/app/data/pr_computation/cz/1czf/1czf.pr.out
profile	/app/data/saxs_computation/cz/1czf/1czf.dat

ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER

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

POLYGALACTURONASE II

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