SAXSdb — 1bug

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

PROTEIN (CATECHOL OXIDASE)

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 1–345	Not recorded	CU COPPER (II) ION × 2 URS N-PHENYLTHIOUREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.273
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–345	Not recorded	CU COPPER (II) ION × 2 URS N-PHENYLTHIOUREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.273

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 1BUG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BT1 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–345（345 aa）	Not recorded	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.256
1BT1 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–345（345 aa）	Not recorded	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.256
1BT2 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–345（345 aa）	Not recorded	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.278
1BT2 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–345（345 aa）	Not recorded	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.278
1BT3 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–345（345 aa）	Not recorded	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	PPO1_IPOBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–345； UniProt 1–345 Author chain B； PDBConstruct 1–345； UniProt 1–345

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	1bug
Deposition date deposition_date	1998-09-03
Structure title title	CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR COMPLEX WITH PHENYLTHIOUREA (PTU)
Keywords keywords	CATECHOL OXIDASE, DICOPPER ENZYME, IPOMOEA BATATAS, OXIDOREDUCTASE; OXIDOREDUCTASE
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	30.64 Å
Radius of gyration Rg (electron density) rg_electron	30.01 Å
Forward intensity I(0) i0	93754200.00
Molecular weight molecular_weight	76064.0 kDa
Excluded volume excluded_volume	94531 Å³
Envelope volume envelope_volume	111410 Å³
Hydration-shell volume shell_volume	31400 Å³
Envelope diameter envelope_diameter	98.5 Å
Shell Rg shell_rg	36.58 Å
Envelope Rg envelope_rg	29.86 Å
Shape Rg shape_rg	30.02 Å
Total Rg total_rg	30.54 Å
Total atoms total_atoms	5356
Residues n_residues	672
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	96.5 Å
Rg (real space) rg_real	30.74 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	9.3750e+07
I(0) uncertainty (real space) i0_real_error	1.5010e+06
Rg (reciprocal space) rg_reciprocal	30.70 Å
I(0) (reciprocal space) i0_reciprocal	93750000.0000
Solution quality estimate total_estimate	0.8689
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.328
Kurtosis Kurtosis kurtosis	-0.767
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34210000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.895

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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	PROTEIN (CATECHOL OXIDASE)
Molecular weight formula_weight	38814.6 kDa
EC 编号 ec_number	1.10.3.1
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	5537

APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLAGKPRKRDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWLDSKP

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	N-PHENYLTHIOUREA
Molecular weight formula_weight	152.2 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	181

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1buga_
Class class	a — All alpha proteins
Fold Fold fold	a.86 — Di-copper centre-containing domain
Superfamily Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
Family Family family	a.86.1.2 — Catechol oxidase

Domain ID domain_id	d1bugb_
Class class	a — All alpha proteins
Fold Fold fold	a.86 — Di-copper centre-containing domain
Superfamily Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
Family Family family	a.86.1.2 — Catechol oxidase

CATH v4.4 (2 domains)

Domain ID domain_id	1bugA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	1bugB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

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8. Citations (1)

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Unit-cell length a length_a	45.820 Å
Unit-cell length b length_b	164.750 Å
Unit-cell length c length_c	52.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1810
R_work r_work	0.1810
R_free r_free	0.2730

fit	/app/data/saxs_computation/bu/1bug/1bug.fit
pddf	/app/data/pr_computation/bu/1bug/1bug.pr.out
profile	/app/data/saxs_computation/bu/1bug/1bug.dat

CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR COMPLEX WITH PHENYLTHIOUREA (PTU)

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

PROTEIN (CATECHOL OXIDASE)

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