1bym

SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR

Method: SOLUTION NMR Dmax: 40.8 Å Quality: REASONABLE

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

PROTEIN (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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 130–226 Fragment:RESIDUES 130-226 No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.5;303 K Resolution not provided

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 1–97; UniProt 130–226

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 1bym

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1bym
Deposition date deposition_date1998-10-17
Structure title titleSOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR
Keywords keywordsREPRESSOR, DTXR, C-TERMINAL DOMAIN, PROKARYOTIC SH3 DOMAIN, TRANSCRIPTION REGULATION, PEPTIDE-BINDING, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier15.13
Radius of gyration Rg (electron density) rg_electron14.76
Forward intensity I(0) i0681481000.00
Molecular weight molecular_weight211760.0 kDa
Excluded volume excluded_volume262260 ų
Envelope volume envelope_volume57700 ų
Hydration-shell volume shell_volume22430 ų
Envelope diameter envelope_diameter74.1
Shell Rg shell_rg28.71
Envelope Rg envelope_rg22.75
Shape Rg shape_rg14.75
Total Rg total_rg15.22
Total atoms total_atoms29660
Residues n_residues1940
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 dmax40.8
Rg (real space) rg_real14.21
Rg uncertainty (real space) rg_real_error0.05
I(0) (real space) i0_real6.4820e+08
I(0) uncertainty (real space) i0_real_error5.0060e+06
Rg (reciprocal space) rg_reciprocal15.24
I(0) (reciprocal space) i0_reciprocal681500000.0000
Solution quality estimate total_estimate0.6726
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary17.0
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.167
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha3.7950
Highest regularization parameter α highest_alpha392000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.936; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1byma_
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 (1 domains)

Domain ID domain_id1bymA00
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)