SAXSdb — 1dj7

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

FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN

Synechocystis sp.

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–118	Not recorded	FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN × 1 （Q55781） SF4 IRON/SULFUR CLUSTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；297 K；AMSO4, SODIUM ACETATE, MGCL2, TRIETHANOLAMINE-CL BUFFER PH 7.3, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.60 Å R-free 0.278

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 1DJ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PU9 Crystal srtucture of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin f Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 9–118（110 aa）	Not recorded	SO4 SULFATE ION × 6 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.65 Å R-free 0.231
2PU9 Crystal srtucture of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin f Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 9–118（110 aa）	Not recorded	SO4 SULFATE ION × 6 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.65 Å R-free 0.231
2PUK Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 9–116（108 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.00 Å R-free 0.284
2PUK Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 9–116（108 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.00 Å R-free 0.284
2PUO Crystal srtucture of the NEM modified ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–116（109 aa）	Not recorded	SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1 NEQ N-ETHYLMALEIMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.255
2PVD Crystal srtucture of the reduced ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 12–118（107 aa）	Not recorded	SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；298 K；pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.95 Å R-free 0.284
2PVG Crystal srtucture of the binary complex between ferredoxin and ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 11–116（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.288
2PVO Crystal srtucture of the ternary complex between thioredoxin f, ferredoxin, and ferredoxin: thioredoxin reductase Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 9–118（110 aa）	Not recorded	SO4 SULFATE ION × 2 SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.263

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q55389_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 2–118

FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN

Synechocystis sp.

UniProt Q55781

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–75	Not recorded	FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN × 1 （Q55389） SF4 IRON/SULFUR CLUSTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；297 K；AMSO4, SODIUM ACETATE, MGCL2, TRIETHANOLAMINE-CL BUFFER PH 7.3, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.60 Å R-free 0.278

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 1DJ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PU9 Crystal srtucture of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin f Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–74（74 aa）	Not recorded	SO4 SULFATE ION × 6 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.65 Å R-free 0.231
2PU9 Crystal srtucture of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin f Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–74（74 aa）	Not recorded	SO4 SULFATE ION × 6 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.65 Å R-free 0.231
2PUK Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–73（73 aa）	Mutation：C40S	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.00 Å R-free 0.284
2PUK Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–73（73 aa）	Mutation：C40S	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.00 Å R-free 0.284
2PUO Crystal srtucture of the NEM modified ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–73（73 aa）	Not recorded	SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1 NEQ N-ETHYLMALEIMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.255
2PVD Crystal srtucture of the reduced ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–73（73 aa）	Not recorded	SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；298 K；pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.95 Å R-free 0.284
2PVG Crystal srtucture of the binary complex between ferredoxin and ferredoxin:thioredoxin reductase Deposited 2007-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–73（73 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.288
2PVO Crystal srtucture of the ternary complex between thioredoxin f, ferredoxin, and ferredoxin: thioredoxin reductase Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–74（74 aa）	Mutation：C49S	SO4 SULFATE ION × 2 SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.263

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FTRV_SYNY3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–75； UniProt 1–75

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	1dj7
Deposition date deposition_date	1999-12-02
Structure title title	CRYSTAL STRUCTURE OF FERREDOXIN THIOREDOXIN REDUCTASE
Keywords keywords	4FE-4S CLUSTER BINDING FOLD WITH CXCX16CXCX8CXC BINDING MOTIF, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	17.99 Å
Radius of gyration Rg (electron density) rg_electron	17.28 Å
Forward intensity I(0) i0	8433860.00
Molecular weight molecular_weight	20356.0 kDa
Excluded volume excluded_volume	24949 Å³
Envelope volume envelope_volume	28924 Å³
Hydration-shell volume shell_volume	14465 Å³
Envelope diameter envelope_diameter	62.8 Å
Shell Rg shell_rg	22.75 Å
Envelope Rg envelope_rg	17.59 Å
Shape Rg shape_rg	17.37 Å
Total Rg total_rg	17.89 Å
Total atoms total_atoms	1409
Residues n_residues	182
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	60.5 Å
Rg (real space) rg_real	18.00 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	8.4340e+06
I(0) uncertainty (real space) i0_real_error	1.0250e+05
Rg (reciprocal space) rg_reciprocal	18.00 Å
I(0) (reciprocal space) i0_reciprocal	8434000.0000
Solution quality estimate total_estimate	0.7932
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.238
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1801000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN
Molecular weight formula_weight	13275.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1556

TSSDTQNNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKASMA

来源 Source

来源生物 organism	Synechocystis sp.
NCBI Class编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN
Molecular weight formula_weight	8570.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLIED

来源 Source

来源生物 organism	Synechocystis sp.
NCBI Class编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dj7a_
Class class	g — Small proteins
Fold Fold fold	g.36 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Superfamily Superfamily superfamily	g.36.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Family Family family	g.36.1.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain

Domain ID domain_id	d1dj7b_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.4 — Electron transport accessory proteins
Family Family family	b.34.4.3 — Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain

CATH v4.4 (2 domains)

Domain ID domain_id	1dj7A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	460 — Ferredoxin Thioredoxin Reductase
Homologous superfamily homologous superfamily	10 — Ferredoxin thioredoxin reductase catalytic beta subunit

Domain ID domain_id	1dj7B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	45.296 Å
Unit-cell length b length_b	45.296 Å
Unit-cell length c length_c	172.147 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2640
R_work r_work	0.2380
R_free r_free	0.2780

fit	/app/data/saxs_computation/dj/1dj7/1dj7.fit
pddf	/app/data/pr_computation/dj/1dj7/1dj7.pr.out
profile	/app/data/saxs_computation/dj/1dj7/1dj7.dat

CRYSTAL STRUCTURE OF FERREDOXIN THIOREDOXIN REDUCTASE

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

FERREDOXIN THIOREDOXIN REDUCTASE: CATALYTIC CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

FERREDOXIN THIOREDOXIN REDUCTASE: VARIABLE CHAIN

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)