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1zzy

Crystal Structure of Thioredoxin Mutant L7V

Method: X-RAY DIFFRACTION Dmax: 58.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thioredoxin 1

Escherichia coli

UniProt P00274

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 1–108 Mutation：L7V No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K Resolution 2.50 Å R-free 0.274
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–108 Mutation：L7V No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K Resolution 2.50 Å R-free 0.274

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 1ZZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M7T Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability Deposited 2002-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 68–107（40 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K
NMR sample composition 1 mM protein in 100 mM sodium phosphate buffer (pH 7.0), 20 M EDTA, 0.02% sodium azide, and 10% D2O. | 90% H2O/10% D2O
Resolution not provided
1OAZ IgE Fv SPE7 complexed with a recombinant thioredoxin Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–34（34 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Chain A 35–108（74 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00
Resolution 2.78 Å R-free 0.276
1OAZ IgE Fv SPE7 complexed with a recombinant thioredoxin Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–34（34 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Chain B 35–108（74 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00
Resolution 2.78 Å R-free 0.276
2BTO Structure of BtubA from Prosthecobacter dejongeii Deposited 2005-06-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain T 1–108（108 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 1.6M NA K PHOSPHATE, PH 6.0
Resolution 2.50 Å R-free 0.235

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

View Construct and Data Evidence
UniProt name THIO_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 1–108 Author chain B； 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 1zzy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1zzy
Deposition date deposition_date2005-06-15
Structure title titleCrystal Structure of Thioredoxin Mutant L7V
Keywords keywordsAlpha/Beta, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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_guinier19.17 Å
Radius of gyration Rg (electron density) rg_electron17.87 Å
Forward intensity I(0) i08805820.00
Molecular weight molecular_weight22910.0 kDa
Excluded volume excluded_volume29168 ų
Envelope volume envelope_volume34406 ų
Hydration-shell volume shell_volume16561 ų
Envelope diameter envelope_diameter58.3 Å
Shell Rg shell_rg23.28 Å
Envelope Rg envelope_rg17.76 Å
Shape Rg shape_rg17.86 Å
Total Rg total_rg18.83 Å
Total atoms total_atoms1614
Residues n_residues212
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 dmax58.5 Å
Rg (real space) rg_real19.08 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real8.8060e+06
I(0) uncertainty (real space) i0_real_error1.1750e+05
Rg (reciprocal space) rg_reciprocal19.10 Å
I(0) (reciprocal space) i0_reciprocal8806000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.4 Å
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.499
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1739000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1zzya_
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_idd1zzyb_
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 (2 domains)

Domain ID domain_id1zzyA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1zzyB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
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8. Citations (1)

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9. Files and Curves (10)