5ef3

RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 25.0 MGy

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: EXCELLENT

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 0.271
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 0.271

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.

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 5ef3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ef3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ef3
Deposition date deposition_date2015-10-23
Structure title titleRADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 25.0 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_guinier36.11
Radius of gyration Rg (electron density) rg_electron34.64
Forward intensity I(0) i0598134000.00
Molecular weight molecular_weight186000.0 kDa
Excluded volume excluded_volume227690 ų
Envelope volume envelope_volume289230 ų
Hydration-shell volume shell_volume65480 ų
Envelope diameter envelope_diameter99.7
Shell Rg shell_rg44.66
Envelope Rg envelope_rg33.55
Shape Rg shape_rg34.60
Total Rg total_rg35.40
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 dmax101.2
Rg (real space) rg_real35.75
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real5.9810e+08
I(0) uncertainty (real space) i0_real_error9.1280e+06
Rg (reciprocal space) rg_reciprocal35.98
I(0) (reciprocal space) i0_reciprocal598300000.0000
Solution quality estimate total_estimate0.9074
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.6
Skewness Skewness skewness-0.121
Kurtosis Kurtosis kurtosis-0.653
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha618900000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.968

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_id5ef3A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3F00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3H00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3I00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3J00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3K00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3L00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3M00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3N00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3O00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3P00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3Q00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3R00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3S00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3T00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3U00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id5ef3V00
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)