← Back to search
1dlm

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA

Method: X-RAY DIFFRACTION Dmax: 108.2 Å Quality: GOOD
▼

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

CATECHOL 1,2-DIOXYGENASE

Acinetobacter sp.

UniProt P07773

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 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

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 1DLM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DLQ STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 INHIBITED BY BOUND MERCURY 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 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
1DLT STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL Deposited 1999-12-12 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 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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 1dlm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dlm
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1dlm
Deposition date deposition_date1999-12-11
Structure title titleSTRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA
Keywords keywordsMETALLOPROTEIN, DIOXYGENASE, AROMATIC COMPOUND DEGRADATION, MIXED ALPHA HELIX/ BETA STRAND, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier30.67 Å
Radius of gyration Rg (electron density) rg_electron30.06 Å
Forward intensity I(0) i080405100.00
Molecular weight molecular_weight69521.0 kDa
Excluded volume excluded_volume86337 ų
Envelope volume envelope_volume105980 ų
Hydration-shell volume shell_volume31195 ų
Envelope diameter envelope_diameter116.0 Å
Shell Rg shell_rg35.44 Å
Envelope Rg envelope_rg30.15 Å
Shape Rg shape_rg30.08 Å
Total Rg total_rg30.49 Å
Total atoms total_atoms4902
Residues n_residues618
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax108.2 Å
Rg (real space) rg_real30.89 Å
Rg uncertainty (real space) rg_real_error1.19 Å
I(0) (real space) i0_real8.0410e+07
I(0) uncertainty (real space) i0_real_error1.4430e+06
Rg (reciprocal space) rg_reciprocal30.80 Å
I(0) (reciprocal space) i0_reciprocal80400000.0000
Solution quality estimate total_estimate0.8325
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis-0.333
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15190000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.703; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.739; Smooth: 0.972
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dlma_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1dlmb_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (2 domains)

Domain ID domain_id1dlmA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1dlmB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
▶

8. Citations (4)

▶

9. Files and Curves (10)