SAXSdb — 1ayf

▼

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

ADRENODOXIN

Bos taurus

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 62–166 Chain B； UniProt 62–166	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 10% GLYCEROL, 100 MM TRIS, PH 7.4, 100MM MGCL2, 20 MG/ML PROTEIN	Resolution 1.85 Å R-free 0.253

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 1AYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJE ADRENODOXIN FROM BOVINE Deposited 1999-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–186（127 aa） Chain B 60–186（127 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.298
1CJE ADRENODOXIN FROM BOVINE Deposited 1999-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 60–186（127 aa） Chain D 60–186（127 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.298
1E6E ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 SYSTEMS Deposited 2000-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 59–186（128 aa）	Mutation：YES	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；HANGING DROP VAPOR-DIFFUSION AT 4 DEGR. 0.5MM COMPLEX IN 100MMTRIS-HCL, PH 7.4, 0.9M AMMONIUMSULFATE.	Resolution 2.30 Å R-free 0.268
1E6E ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 SYSTEMS Deposited 2000-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 59–186（128 aa）	Mutation：YES	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；HANGING DROP VAPOR-DIFFUSION AT 4 DEGR. 0.5MM COMPLEX IN 100MMTRIS-HCL, PH 7.4, 0.9M AMMONIUMSULFATE.	Resolution 2.30 Å R-free 0.268
1L6U NMR STRUCTURE OF OXIDIZED ADRENODOXIN Deposited 2002-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–186（128 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	SOLUTION NMR NMR measurement conditions pH 7.4；300 K；Ionic strength (raw mmCIF value) 100 mM salt；Pressure 1 NMR sample composition 2-3mM Adrenodoxin 15N,13C, 50 mM phosphate buffer, 50mM NaCl, 10% D2O, 0.04% NaN3 \| 90% H2O/10% D2O	Resolution not provided
1L6V STRUCTURE OF REDUCED BOVINE ADRENODOXIN Deposited 2002-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–186（128 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	SOLUTION NMR NMR measurement conditions pH 7.4；300 K；Ionic strength (raw mmCIF value) 100mM salt；Pressure 1 NMR sample composition 2-3mM Adrenodoxin, 0mM Phosphate, 50mM NaCl, Dithionite, 10% D2O, 90% H2O, 0.04% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2BT6 Ru(bpy)2(mbpy)-Modified Bovine Adrenodoxin Deposited 2005-05-26	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 63–166（104 aa） Fragment：RESIDUES 63-166	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1 RUA (4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE) × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；30% PEG 4000, 10% GLYCEROL, 10MM TRIS, PH 7.4, 10MM MGCL2, 20 MG/ML PROTEIN	Resolution 1.50 Å R-free 0.186
2BT6 Ru(bpy)2(mbpy)-Modified Bovine Adrenodoxin Deposited 2005-05-26	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 63–166（104 aa） Fragment：RESIDUES 63-166	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1 RUA (4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE) × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；30% PEG 4000, 10% GLYCEROL, 10MM TRIS, PH 7.4, 10MM MGCL2, 20 MG/ML PROTEIN	Resolution 1.50 Å R-free 0.186
2JQR Solution model of crosslinked complex of cytochrome c and adrenodoxin Deposited 2007-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 62–166（105 aa） Fragment：2Fe-2S ferredoxin-type domain, residues 62-166	Mutation：L80C, C95S	HEC HEME C × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	SOLUTION NMR NMR measurement conditions pH 7.4；285 K；Pressure ambient NMR measurement conditions pH 7.4；301 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient NMR sample composition 0.4 mM [U-98% 15N] CcV28C, 0.2-0.6 mM AdxL80C, 20 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [U-98% 15N] AdxL80C, 0.2-0.6 mM CcV28C, 20 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-98% 15N] CcV28C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-98% 15N] AdxL80C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	ADX1_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 62–166 Author chain B； PDBConstruct 1–105； UniProt 62–166

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	1ayf
Deposition date deposition_date	1997-11-03
Structure title title	BOVINE ADRENODOXIN (OXIDIZED)
Keywords keywords	[2FE-2S]FERREDOXIN, ADRENODOXIN, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.47 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	10856500.00
Molecular weight molecular_weight	23294.0 kDa
Excluded volume excluded_volume	28621 Å³
Envelope volume envelope_volume	34215 Å³
Hydration-shell volume shell_volume	15705 Å³
Envelope diameter envelope_diameter	70.2 Å
Shell Rg shell_rg	24.39 Å
Envelope Rg envelope_rg	19.46 Å
Shape Rg shape_rg	19.27 Å
Total Rg total_rg	19.71 Å
Total atoms total_atoms	1606
Residues n_residues	207
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	68.3 Å
Rg (real space) rg_real	19.56 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.0860e+07
I(0) uncertainty (real space) i0_real_error	1.4530e+05
Rg (reciprocal space) rg_reciprocal	19.55 Å
I(0) (reciprocal space) i0_reciprocal	10860000.0000
Solution quality estimate total_estimate	0.8293
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.478
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4523000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.981

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ADRENODOXIN
Molecular weight formula_weight	11661.2 kDa
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	1831

EDKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ayfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d1ayfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

CATH v4.4 (2 domains)

Domain ID domain_id	1ayfA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	1ayfB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	44.180 Å
Unit-cell length b length_b	78.340 Å
Unit-cell length c length_c	60.600 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	11.000 Å
R factor r_factor	0.1930
R_work r_work	0.1950
R_free r_free	0.2530

fit	/app/data/saxs_computation/ay/1ayf/1ayf.fit
pddf	/app/data/pr_computation/ay/1ayf/1ayf.pr.out
profile	/app/data/saxs_computation/ay/1ayf/1ayf.dat

BOVINE ADRENODOXIN (OXIDIZED)

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

ADRENODOXIN

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