1f6m

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THIOREDOXIN, AND THE NADP+ ANALOG, AADP+

Method: X-RAY DIFFRACTION Dmax: 127.1 Å Quality: GOOD

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

THIOREDOXIN REDUCTASE

Escherichia coli

UniProt P0A9P4

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–320 Chain B; UniProt 1–320 Mutation:C135S THIOREDOXIN 1 × 2 (P0AA25) FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 3AA 3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;295 K;cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.95 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–320 Chain F; UniProt 1–320 Mutation:C135S THIOREDOXIN 1 × 2 (P0AA25) FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 3AA 3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;295 K;cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.95 Å R-free 0.247

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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRXB_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–320; UniProt 1–320 Author chain B; PDBConstruct 1–320; UniProt 1–320 Author chain E; PDBConstruct 1–320; UniProt 1–320 Author chain F; PDBConstruct 1–320; UniProt 1–320

THIOREDOXIN 1

Escherichia coli

UniProt P0AA25

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–108 Chain D; UniProt 1–108 Mutation:C35S THIOREDOXIN REDUCTASE × 2 (P0A9P4) FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 3AA 3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;295 K;cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.95 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 1–108 Chain H; UniProt 1–108 Mutation:C35S THIOREDOXIN REDUCTASE × 2 (P0A9P4) FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 3AA 3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;295 K;cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.95 Å R-free 0.247

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.

52 other PDB entries and 99 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–108; UniProt 1–108 Author chain D; PDBConstruct 1–108; UniProt 1–108 Author chain G; PDBConstruct 1–108; UniProt 1–108 Author chain H; PDBConstruct 1–108; UniProt 1–108

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 1f6m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1f6m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1f6m
Deposition date deposition_date2000-06-22
Structure title titleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THIOREDOXIN, AND THE NADP+ ANALOG, AADP+
Keywords keywordsALTERNATE CONFORMATION, TERNARY COMPLEX, DOMAIN MOTION, redox-active center, NADP, FAD, electron transport, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier40.88
Radius of gyration Rg (electron density) rg_electron40.87
Forward intensity I(0) i0577091000.00
Molecular weight molecular_weight190480.0 kDa
Excluded volume excluded_volume235870 ų
Envelope volume envelope_volume305530 ų
Hydration-shell volume shell_volume62642 ų
Envelope diameter envelope_diameter135.1
Shell Rg shell_rg45.61
Envelope Rg envelope_rg40.56
Shape Rg shape_rg40.90
Total Rg total_rg41.01
Total atoms total_atoms13376
Residues n_residues1712
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.1
Rg (real space) rg_real40.86
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real5.7710e+08
I(0) uncertainty (real space) i0_real_error1.0560e+07
Rg (reciprocal space) rg_reciprocal40.88
I(0) (reciprocal space) i0_reciprocal577100000.0000
Solution quality estimate total_estimate0.8673
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.6
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.344
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66000000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.418

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1f6ma1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6ma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase
Domain ID domain_idd1f6md_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase
Domain ID domain_idd1f6me1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6me2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd1f6mg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase
Domain ID domain_idd1f6mh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase

CATH v4.4 (12 domains)

Domain ID domain_id1f6mA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mA02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mB01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mB02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1f6mD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1f6mE01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mE02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mF01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mF02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1f6mG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1f6mH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin

8. Citations (3)

9. Files and Curves (10)