SAXSdb — 1dlt

▼

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

CATECHOL 1,2-DIOXYGENASE

Acinetobacter sp.

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 1–311 Chain B； UniProt 1–311	Not recorded	FE FE (III) ION × 2 CAQ CATECHOL × 2 LIO [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10-15% Peg5000, 100mM Tris-HCl, pH 7.5, .2M MgAcetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.228

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 1DLT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DLM STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA Deposited 1999-12-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–311（311 aa） Chain B 1–311（311 aa）	Not recorded	FE FE (III) ION × 2 LIO [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10-15% Peg5000, 100mM Tris-HCl pH 7.5, 0.2M Mg Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.243
1DLQ STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 INHIBITED BY BOUND MERCURY Deposited 1999-12-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–311（311 aa） Chain B 1–311（311 aa）	Not recorded	FE FE (III) ION × 2 HG MERCURY (II) ION × 6 LIO [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10-15% Peg5000, 100mM Tris-HCl, pH 7.5, .2M MgAcetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.224
1DMH STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL Deposited 1999-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–311（311 aa） Chain B 1–311（311 aa）	Not recorded	FE FE (III) ION × 2 MCT 4-METHYLCATECHOL × 2 LIO [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10-15% PEG5000, 100MM TRIS-HCL, PH 7.5, .2M MGACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.218

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

View Construct and Data Evidence

UniProt name	CATA_ACIAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 1–311 Author chain B； PDBConstruct 1–311； UniProt 1–311

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dlt
Deposition date deposition_date	1999-12-12
Structure title title	STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL
Keywords keywords	METALLOENZYME, DIOXYGENASE, AROMATIC HYDROCARBON DEGREDATION, ALPHA/BETA MOTIF, SUBSTRATE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.59 Å
Radius of gyration Rg (electron density) rg_electron	29.97 Å
Forward intensity I(0) i0	80763200.00
Molecular weight molecular_weight	69741.0 kDa
Excluded volume excluded_volume	86633 Å³
Envelope volume envelope_volume	106480 Å³
Hydration-shell volume shell_volume	31348 Å³
Envelope diameter envelope_diameter	116.3 Å
Shell Rg shell_rg	35.38 Å
Envelope Rg envelope_rg	30.11 Å
Shape Rg shape_rg	29.98 Å
Total Rg total_rg	30.40 Å
Total atoms total_atoms	4918
Residues n_residues	618
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

▼

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

Maximum dimension Dmax dmax	108.7 Å
Rg (real space) rg_real	30.81 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	8.0760e+07
I(0) uncertainty (real space) i0_real_error	1.3350e+06
Rg (reciprocal space) rg_reciprocal	30.72 Å
I(0) (reciprocal space) i0_reciprocal	80760000.0000
Solution quality estimate total_estimate	0.8271
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.505
Kurtosis Kurtosis kurtosis	-0.331
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15560000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.689; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.725; Smooth: 0.958

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CATECHOL 1,2-DIOXYGENASE
Molecular weight formula_weight	34384.1 kDa
EC 编号 ec_number	1.13.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5164

MEVKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV

来源 Source

来源生物 organism	Acinetobacter sp.
NCBI Class编号 ncbi_taxonomy_id	62977
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CATECHOL
Molecular weight formula_weight	110.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE
Molecular weight formula_weight	636.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dlta_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d1dltb_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (2 domains)

Domain ID domain_id	1dltA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	1dltB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

▶

8. Citations (4)

▶

Unit-cell length a length_a	52.800 Å
Unit-cell length b length_b	87.500 Å
Unit-cell length c length_c	84.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.30 °
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	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2280

fit	/app/data/saxs_computation/dl/1dlt/1dlt.fit
pddf	/app/data/pr_computation/dl/1dlt/1dlt.pr.out
profile	/app/data/saxs_computation/dl/1dlt/1dlt.dat

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL

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

CATECHOL 1,2-DIOXYGENASE

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