5eeu

RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 1.31 MGy

Method: X-RAY DIFFRACTION Dmax: 98.1 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 × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain A; UniProt 1–74 Chain B; UniProt 1–74 Chain C; UniProt 1–74 Chain D; UniProt 1–74 Chain E; UniProt 1–74 Chain F; UniProt 1–74 Chain G; UniProt 1–74 Chain H; UniProt 1–74 Chain I; UniProt 1–74 Chain J; UniProt 1–74 Chain K; UniProt 1–74 Not recorded TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293.15 K;Potassium phosphate,L-tryptophan,potassium glutamate,triethanolamine,MgCl2,monomethyl ether PEG 2000 Resolution 1.98 Å R-free 0.232
2 Protein–RNA Homooligomer Protein × 11 RNA 1 PDB declaration: dodecameric(12) Consistent with all polymer counts Chain L; UniProt 1–74 Chain M; UniProt 1–74 Chain N; UniProt 1–74 Chain O; UniProt 1–74 Chain P; UniProt 1–74 Chain Q; UniProt 1–74 Chain R; UniProt 1–74 Chain S; UniProt 1–74 Chain T; UniProt 1–74 Chain U; UniProt 1–74 Chain V; UniProt 1–74 Not recorded (GAGUU)10GAG 53-NUCLEOTIDE RNA × 1 TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293.15 K;Potassium phosphate,L-tryptophan,potassium glutamate,triethanolamine,MgCl2,monomethyl ether PEG 2000 Resolution 1.98 Å R-free 0.232

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 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTRB_GEOSE
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 Author chain D; PDBConstruct 1–74; UniProt 1–74 Author chain E; PDBConstruct 1–74; UniProt 1–74 Author chain F; PDBConstruct 1–74; UniProt 1–74 Author chain G; PDBConstruct 1–74; UniProt 1–74 Author chain H; PDBConstruct 1–74; UniProt 1–74 Author chain I; PDBConstruct 1–74; UniProt 1–74 Author chain J; PDBConstruct 1–74; UniProt 1–74 Author chain K; PDBConstruct 1–74; UniProt 1–74 Author chain L; PDBConstruct 1–74; UniProt 1–74 Author chain M; PDBConstruct 1–74; UniProt 1–74 Author chain N; PDBConstruct 1–74; UniProt 1–74 Author chain O; PDBConstruct 1–74; UniProt 1–74 Author chain P; PDBConstruct 1–74; UniProt 1–74 Author chain Q; PDBConstruct 1–74; UniProt 1–74 Author chain R; PDBConstruct 1–74; UniProt 1–74 Author chain S; PDBConstruct 1–74; UniProt 1–74 Author chain T; PDBConstruct 1–74; UniProt 1–74 Author chain U; PDBConstruct 1–74; UniProt 1–74 Author chain V; 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 5eeu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5eeu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5eeu
Deposition date deposition_date2015-10-23
Structure title titleRADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 1.31 MGy
Keywords keywordsprotein-RNA complex, radiation damage, 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_guinier35.99
Radius of gyration Rg (electron density) rg_electron34.52
Forward intensity I(0) i0598443000.00
Molecular weight molecular_weight186000.0 kDa
Excluded volume excluded_volume227690 ų
Envelope volume envelope_volume287890 ų
Hydration-shell volume shell_volume65350 ų
Envelope diameter envelope_diameter99.4
Shell Rg shell_rg44.54
Envelope Rg envelope_rg33.47
Shape Rg shape_rg34.47
Total Rg total_rg35.27
Total atoms total_atoms13087
Residues n_residues1565
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 dmax98.1
Rg (real space) rg_real35.64
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real5.9840e+08
I(0) uncertainty (real space) i0_real_error8.1850e+06
Rg (reciprocal space) rg_reciprocal35.86
I(0) (reciprocal space) i0_reciprocal598600000.0000
Solution quality estimate total_estimate0.8384
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.3
Skewness Skewness skewness-0.117
Kurtosis Kurtosis kurtosis-0.651
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha635000000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.974; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 22 domains

CATH v4.4 (22 domains)

Domain ID domain_id5eeuA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuM00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuO00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuP00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuR00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuS00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuT00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuU00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5eeuV00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like

8. Citations (2)

9. Files and Curves (10)