1g3s

CYS102SER DTXR

Method: X-RAY DIFFRACTION Dmax: 70.1 Å Quality: GOOD

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

DIPHTHERIA TOXIN REPRESSOR

Corynebacterium diphtheriae

UniProt P33120

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 1–226 Mutation:C102S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;298 K;Ammonium sulfate, EDTA, glycerol, pH 8.5, VAPOR DIFFUSION, temperature 298K Resolution 2.40 Å R-free 0.271

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.

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DTXR_CORDI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–226; UniProt 1–226

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 1g3s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1g3s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1g3s
Deposition date deposition_date2000-10-25
Structure title titleCYS102SER DTXR
Keywords keywordsDNA binding protein, iron dependent regulator, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.72
Radius of gyration Rg (electron density) rg_electron21.21
Forward intensity I(0) i09653700.00
Molecular weight molecular_weight22614.0 kDa
Excluded volume excluded_volume28087 ų
Envelope volume envelope_volume35150 ų
Hydration-shell volume shell_volume14878 ų
Envelope diameter envelope_diameter70.6
Shell Rg shell_rg26.03
Envelope Rg envelope_rg21.12
Shape Rg shape_rg21.24
Total Rg total_rg21.83
Total atoms total_atoms1590
Residues n_residues212
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 dmax70.1
Rg (real space) rg_real21.85
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real9.6540e+06
I(0) uncertainty (real space) i0_real_error1.3240e+05
Rg (reciprocal space) rg_reciprocal21.83
I(0) (reciprocal space) i0_reciprocal9654000.0000
Solution quality estimate total_estimate0.8517
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.8
Skewness Skewness skewness0.361
Kurtosis Kurtosis kurtosis-0.646
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4573000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.768; Smooth: 0.972

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1g3sa1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.24 — Iron-dependent repressor protein
Domain ID domain_idd1g3sa2
Class classa — All alpha proteins
Fold Fold folda.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamilya.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family familya.76.1.1 — Iron-dependent repressor protein, dimerization domain
Domain ID domain_idd1g3sa3
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.1 — C-terminal domain of transcriptional repressors
Family Family familyb.34.1.2 — FeoA-like

CATH v4.4 (3 domains)

Domain ID domain_id1g3sA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1g3sA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily10 — Iron dependent repressor, metal binding and dimerisation domain
Domain ID domain_id1g3sA03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily90 — Ferrous iron transport protein A (FeoA)

8. Citations (1)

9. Files and Curves (10)