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1dhy

KKS102 BPHC ENZYME

Method: X-RAY DIFFRACTION Dmax: 58.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE

Pseudomonas sp.

UniProt P17297

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 1–292 Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.30 Å R-free 0.246
2 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–292 Not recorded FE FE (III) ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.30 Å R-free 0.246

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 1DHY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EIL 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE Deposited 2000-02-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–292（292 aa）
Not recorded SO4 SULFATE ION × 8 FE FE (III) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；285 K；285 K, Tris/HCl Ammonium sulfate hexylene glycol, pH 7.5, temperature 285.0K
Resolution 2.00 Å R-free 0.253
1EIQ 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE Deposited 2000-02-28 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–292（292 aa）
Not recorded FE FE (III) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；285 K；285K, Tris/HCl, Ammonium sulfate, hexylene glycol, pH 7.5
Resolution 2.00 Å R-free 0.228
1EIR 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE Deposited 2000-02-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–292（292 aa）
Not recorded FE FE (III) ION × 8 BPY BIPHENYL-2,3-DIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Batch method；pH 7.5；285 K；285K, Tris/HCl, Ammonium sulfate, hexylene glycol, pH 7.5, Batch method
Resolution 2.00 Å R-free 0.231
1KW3 Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution Deposited 2002-01-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Not recorded FE2 FE (II) ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions Batch method；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch method, temperature 285K
Resolution 1.45 Å R-free 0.177
1KW6 Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution Deposited 2002-01-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Not recorded FE2 FE (II) ION × 8 BPY BIPHENYL-2,3-DIOL × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions Batch；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Resolution 1.45 Å R-free 0.171
1KW8 Crystal structure of BphC-2,3-dihydroxybiphenyl-NO complex Deposited 2002-01-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Not recorded FE2 FE (II) ION × 8 NO NITRIC OXIDE × 8 BPY BIPHENYL-2,3-DIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Batch；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Resolution 2.00 Å R-free 0.184
1KW9 Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution Deposited 2002-01-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Not recorded FE2 FE (II) ION × 8 BPY BIPHENYL-2,3-DIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Batch；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Resolution 1.95 Å R-free 0.183
1KWB Crystal structure of the His145Ala mutant of 2,3-dihydroxybipheny dioxygenase (BphC) Deposited 2002-01-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Mutation：H145A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Batch；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Resolution 2.00 Å R-free 0.175
1KWC The His145Ala mutant of 2,3-dihydroxybiphenyl dioxygenase in complex with 2,3-dihydroxybiphenyl Deposited 2002-01-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain B 1–292（292 aa）
Mutation：H145A BPY BIPHENYL-2,3-DIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Batch；pH 7.5；285 K；Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Resolution 2.10 Å R-free 0.201

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPHC_PSES1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–292； UniProt 1–292

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 1dhy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dhy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dhy
Deposition date deposition_date1995-07-07
Structure title titleKKS102 BPHC ENZYME
Keywords keywordsEXTRADIOL TYPE DIOXYGENASE, OXIDOREDUCTASE (OXYGENASE); OXIDOREDUCTASE (OXYGENASE)
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.82 Å
Radius of gyration Rg (electron density) rg_electron17.68 Å
Forward intensity I(0) i016137300.00
Molecular weight molecular_weight30525.0 kDa
Excluded volume excluded_volume38215 ų
Envelope volume envelope_volume42205 ų
Hydration-shell volume shell_volume19553 ų
Envelope diameter envelope_diameter58.6 Å
Shell Rg shell_rg24.32 Å
Envelope Rg envelope_rg17.87 Å
Shape Rg shape_rg17.67 Å
Total Rg total_rg18.67 Å
Total atoms total_atoms2153
Residues n_residues278
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.4 Å
Rg (real space) rg_real18.68 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real1.6140e+07
I(0) uncertainty (real space) i0_real_error1.8000e+05
Rg (reciprocal space) rg_reciprocal18.70 Å
I(0) (reciprocal space) i0_reciprocal16140000.0000
Solution quality estimate total_estimate0.8949
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.8 Å
Skewness Skewness skewness0.089
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2762000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.974
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dhya1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamilyd.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family familyd.32.1.3 — Extradiol dioxygenases
Domain ID domain_idd1dhya2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamilyd.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family familyd.32.1.3 — Extradiol dioxygenases

CATH v4.4 (2 domains)

Domain ID domain_id1dhyA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
Domain ID domain_id1dhyA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
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8. Citations (1)

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9. Files and Curves (10)