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3ozu

The Crystal Structure of flavohemoglobin from R. eutrophus in complex with miconazole

Method: X-RAY DIFFRACTION Dmax: 70.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Flavohemoprotein

Ralstonia eutropha

UniProt P39662

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 1–403 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X89 1-[(2R)-2-[(2,4-dichlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–403 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X89 1-[(2R)-2-[(2,4-dichlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.233

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 3OZU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CQX Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution Deposited 1999-08-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–403（403 aa）
Not recorded NA SODIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 1.75 Å R-free 0.215
1CQX Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution Deposited 1999-08-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–403（403 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 1.75 Å R-free 0.215
1CQX Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution Deposited 1999-08-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Chain B 1–403（403 aa）
Not recorded NA SODIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 1.75 Å R-free 0.215
3OZV The Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole Deposited 2010-09-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–403（403 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 1 ECN 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.248
3OZV The Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole Deposited 2010-09-27 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–403（403 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 1 ECN 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.248
3OZV The Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole Deposited 2010-09-27 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Chain B 1–403（403 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 2 ECN 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.248
3OZW The Crystal Structure of flavohemoglobin from R. eutrophus in complex with ketoconazole Deposited 2010-09-27 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Chain B 1–403（403 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 KKK 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine × 2 DGG 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；277 K；1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.30 Å R-free 0.241

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HMP_RALEH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–403； UniProt 1–403

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 3ozu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ozu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ozu
Deposition date deposition_date2010-09-27
Structure title titleThe Crystal Structure of flavohemoglobin from R. eutrophus in complex with miconazole
Keywords keywordsglobin fold, antiparallel beta-barrel, alpha/beta fold, HEM-, FAD-, NAD- binding domains, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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_guinier22.86 Å
Radius of gyration Rg (electron density) rg_electron21.82 Å
Forward intensity I(0) i037030700.00
Molecular weight molecular_weight46682.0 kDa
Excluded volume excluded_volume58248 ų
Envelope volume envelope_volume68563 ų
Hydration-shell volume shell_volume25962 ų
Envelope diameter envelope_diameter72.2 Å
Shell Rg shell_rg28.92 Å
Envelope Rg envelope_rg21.80 Å
Shape Rg shape_rg21.82 Å
Total Rg total_rg22.68 Å
Total atoms total_atoms3283
Residues n_residues403
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 dmax70.9 Å
Rg (real space) rg_real22.73 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real3.7030e+07
I(0) uncertainty (real space) i0_real_error4.3870e+05
Rg (reciprocal space) rg_reciprocal22.77 Å
I(0) (reciprocal space) i0_reciprocal37030000.0000
Solution quality estimate total_estimate0.9055
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7075000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3ozua1
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.0 — automated matches
Domain ID domain_idd3ozua2
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.0 — automated matches
Domain ID domain_idd3ozua3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id3ozuA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id3ozuA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id3ozuA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (1)

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9. Files and Curves (10)