2zd0

Crystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP)

Method: X-RAY DIFFRACTION Dmax: 64.7 Å Quality: GOOD

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

Transcription attenuation protein mtrB

Geobacillus stearothermophilus

UniProt Q9X6J6

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 × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 1–74 Chain B; UniProt 1–74 Chain C; UniProt 1–74 Not recorded TRP TRYPTOPHAN × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 10.5;293 K;0.09M CAPS pH 10.5, 30%(w/v) PEG300, 0.15M Ammonium sulfate, 10mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.50 Å R-free 0.256

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.

27 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTRB_BACST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–74; UniProt 1–74 Author chain B; PDBConstruct 1–74; UniProt 1–74 Author chain C; PDBConstruct 1–74; UniProt 1–74

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 2zd0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zd0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zd0
Deposition date deposition_date2007-11-15
Structure title titleCrystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP)
Keywords keywordsLINKER, ARTIFICIAL, ENGINEERED, RING PROTEIN, 12-mer, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.16
Radius of gyration Rg (electron density) rg_electron17.00
Forward intensity I(0) i08995190.00
Molecular weight molecular_weight22104.0 kDa
Excluded volume excluded_volume27757 ų
Envelope volume envelope_volume32071 ų
Hydration-shell volume shell_volume16107 ų
Envelope diameter envelope_diameter64.3
Shell Rg shell_rg22.94
Envelope Rg envelope_rg17.35
Shape Rg shape_rg16.98
Total Rg total_rg18.06
Total atoms total_atoms1564
Residues n_residues195
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 dmax64.7
Rg (real space) rg_real18.12
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real8.9950e+06
I(0) uncertainty (real space) i0_real_error1.0560e+05
Rg (reciprocal space) rg_reciprocal18.12
I(0) (reciprocal space) i0_reciprocal8995000.0000
Solution quality estimate total_estimate0.7579
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.6
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.017
Angular range angular_range— – 0.4400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2366000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.619; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2zd0a_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.5 — TRAP-like
Family Family familyb.82.5.1 — Trp RNA-binding attenuation protein (TRAP)
Domain ID domain_idd2zd0b_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.5 — TRAP-like
Family Family familyb.82.5.1 — Trp RNA-binding attenuation protein (TRAP)
Domain ID domain_idd2zd0c_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.5 — TRAP-like
Family Family familyb.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

CATH v4.4 (3 domains)

Domain ID domain_id2zd0A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zd0B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zd0C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like

8. Citations (1)

9. Files and Curves (10)