SAXSdb — 3ozw

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

Flavohemoglobin

Ralstonia eutropha

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 1–403 Chain B； UniProt 1–403	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

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 3OZW	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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 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
3OZU The Crystal Structure of flavohemoglobin from R. eutrophus in complex with miconazole Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state 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 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
3OZU The Crystal Structure of flavohemoglobin from R. eutrophus in complex with miconazole Deposited 2010-09-27	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–403（403 aa）	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
3OZV The Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 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

3 other PDB entries and 8 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 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ozw
Deposition date deposition_date	2010-09-27
Structure title title	The Crystal Structure of flavohemoglobin from R. eutrophus in complex with ketoconazole
Keywords keywords	globin fold, antiparallel beta-barrel, alpha/beta fold, HEM-, FAD-, NAD- binding domains, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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	30.38 Å
Radius of gyration Rg (electron density) rg_electron	29.57 Å
Forward intensity I(0) i0	138691000.00
Molecular weight molecular_weight	93734.0 kDa
Excluded volume excluded_volume	117260 Å³
Envelope volume envelope_volume	142960 Å³
Hydration-shell volume shell_volume	39851 Å³
Envelope diameter envelope_diameter	99.5 Å
Shell Rg shell_rg	37.30 Å
Envelope Rg envelope_rg	29.40 Å
Shape Rg shape_rg	29.56 Å
Total Rg total_rg	30.29 Å
Total atoms total_atoms	6600
Residues n_residues	806
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	96.6 Å
Rg (real space) rg_real	30.33 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.3870e+08
I(0) uncertainty (real space) i0_real_error	2.1920e+06
Rg (reciprocal space) rg_reciprocal	30.35 Å
I(0) (reciprocal space) i0_reciprocal	138700000.0000
Solution quality estimate total_estimate	0.8998
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42000000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Flavohemoglobin
Molecular weight formula_weight	44831.9 kDa
EC 编号 ec_number	1.14.12.17
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	6795

MLTQKTKDIVKATAPVLAEHGYDIIKCFYQRMFEAHPELKNVFNMAHQEQGQQQQALARAVYAYAENIEDPNSLMAVLKNIANKHASLGVKPEQYPIVGEHLLAAIKEVLGNAATDDIISAWAQAYGNLADVLMGMESELYERSAEQPGGWKGWRTFVIREKRPESDVITSFILEPADGGPVVNFEPGQYTSVAIDVPALGLQQIRQYSLSDMPNGRSYRISVKREGGGPQPPGYVSNLLHDHVNVGDQVKLAAPYGSFHIDVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFVFYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFAE

来源 Source

来源生物 organism	Ralstonia eutropha
通用名 common_name	Cupriavidus necator
NCBI Class编号 ncbi_taxonomy_id	381666
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
Molecular weight formula_weight	531.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
Molecular weight formula_weight	735.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3ozwa1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d3ozwa2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3ozwa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

Domain ID domain_id	d3ozwb1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d3ozwb2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3ozwb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3ozwA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3ozwA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3ozwA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	3ozwB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3ozwB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3ozwB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

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8. Citations (1)

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Unit-cell length a length_a	87.120 Å
Unit-cell length b length_b	87.120 Å
Unit-cell length c length_c	292.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2410

fit	/app/data/saxs_computation/oz/3ozw/3ozw.fit
pddf	/app/data/pr_computation/oz/3ozw/3ozw.pr.out
profile	/app/data/saxs_computation/oz/3ozw/3ozw.dat

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