4v4f

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats

Method: X-RAY DIFFRACTION Dmax: 152.7 Å Quality: GOOD

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

TRANSCRIPTION ATTENUATION PROTEIN MTRB

BACILLUS 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–RNA Homooligomer Protein × 11 RNA 11 PDB declaration: 22-meric(22) Consistent with all polymer counts Chain AA; UniProt 1–74 Chain AB; UniProt 1–74 Chain AC; UniProt 1–74 Chain AD; UniProt 1–74 Chain AE; UniProt 1–74 Chain AF; UniProt 1–74 Chain AG; UniProt 1–74 Chain AH; UniProt 1–74 Chain AI; UniProt 1–74 Chain AJ; UniProt 1–74 Chain AK; UniProt 1–74 Not recorded 5'-R(*UP*AP*GP*AP*UP)-3' × 11 TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00 Resolution 1.90 Å R-free 0.236
2 Protein homooligomer Homooligomer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain AL; UniProt 1–74 Chain AM; UniProt 1–74 Chain AN; UniProt 1–74 Chain AO; UniProt 1–74 Chain AP; UniProt 1–74 Chain AQ; UniProt 1–74 Chain AR; UniProt 1–74 Chain AS; UniProt 1–74 Chain AT; UniProt 1–74 Chain AU; UniProt 1–74 Chain AV; UniProt 1–74 Not recorded TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00 Resolution 1.90 Å R-free 0.236
3 Protein–RNA Homooligomer Protein × 11 RNA 11 PDB declaration: 22-meric(22) Consistent with all polymer counts Chain BA; UniProt 1–74 Chain BB; UniProt 1–74 Chain BC; UniProt 1–74 Chain BD; UniProt 1–74 Chain BE; UniProt 1–74 Chain BF; UniProt 1–74 Chain BG; UniProt 1–74 Chain BH; UniProt 1–74 Chain BI; UniProt 1–74 Chain BJ; UniProt 1–74 Chain BK; UniProt 1–74 Not recorded 5'-R(*UP*AP*GP*AP*UP)-3' × 11 TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00 Resolution 1.90 Å R-free 0.236
4 Protein homooligomer Homooligomer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain BL; UniProt 1–74 Chain BM; UniProt 1–74 Chain BN; UniProt 1–74 Chain BO; UniProt 1–74 Chain BP; UniProt 1–74 Chain BQ; UniProt 1–74 Chain BR; UniProt 1–74 Chain BS; UniProt 1–74 Chain BT; UniProt 1–74 Chain BU; UniProt 1–74 Chain BV; UniProt 1–74 Not recorded TRP TRYPTOPHAN × 11 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00 Resolution 1.90 Å R-free 0.236

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 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTRB_BACST
Isoform
PDB entities 2
Chains and sequence ranges Author chain AA; PDBConstruct 1–74; UniProt 1–74 Author chain AB; PDBConstruct 1–74; UniProt 1–74 Author chain AC; PDBConstruct 1–74; UniProt 1–74 Author chain AD; PDBConstruct 1–74; UniProt 1–74 Author chain AE; PDBConstruct 1–74; UniProt 1–74 Author chain AF; PDBConstruct 1–74; UniProt 1–74 Author chain AG; PDBConstruct 1–74; UniProt 1–74 Author chain AH; PDBConstruct 1–74; UniProt 1–74 Author chain AI; PDBConstruct 1–74; UniProt 1–74 Author chain AJ; PDBConstruct 1–74; UniProt 1–74 Author chain AK; PDBConstruct 1–74; UniProt 1–74 Author chain AL; PDBConstruct 1–74; UniProt 1–74 Author chain AM; PDBConstruct 1–74; UniProt 1–74 Author chain AN; PDBConstruct 1–74; UniProt 1–74 Author chain AO; PDBConstruct 1–74; UniProt 1–74 Author chain AP; PDBConstruct 1–74; UniProt 1–74 Author chain AQ; PDBConstruct 1–74; UniProt 1–74 Author chain AR; PDBConstruct 1–74; UniProt 1–74 Author chain AS; PDBConstruct 1–74; UniProt 1–74 Author chain AT; PDBConstruct 1–74; UniProt 1–74 Author chain AU; PDBConstruct 1–74; UniProt 1–74 Author chain AV; PDBConstruct 1–74; UniProt 1–74 Author chain BA; PDBConstruct 1–74; UniProt 1–74 Author chain BB; PDBConstruct 1–74; UniProt 1–74 Author chain BC; PDBConstruct 1–74; UniProt 1–74 Author chain BD; PDBConstruct 1–74; UniProt 1–74 Author chain BE; PDBConstruct 1–74; UniProt 1–74 Author chain BF; PDBConstruct 1–74; UniProt 1–74 Author chain BG; PDBConstruct 1–74; UniProt 1–74 Author chain BH; PDBConstruct 1–74; UniProt 1–74 Author chain BI; PDBConstruct 1–74; UniProt 1–74 Author chain BJ; PDBConstruct 1–74; UniProt 1–74 Author chain BK; PDBConstruct 1–74; UniProt 1–74 Author chain BL; PDBConstruct 1–74; UniProt 1–74 Author chain BM; PDBConstruct 1–74; UniProt 1–74 Author chain BN; PDBConstruct 1–74; UniProt 1–74 Author chain BO; PDBConstruct 1–74; UniProt 1–74 Author chain BP; PDBConstruct 1–74; UniProt 1–74 Author chain BQ; PDBConstruct 1–74; UniProt 1–74 Author chain BR; PDBConstruct 1–74; UniProt 1–74 Author chain BS; PDBConstruct 1–74; UniProt 1–74 Author chain BT; PDBConstruct 1–74; UniProt 1–74 Author chain BU; PDBConstruct 1–74; UniProt 1–74 Author chain BV; 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 4v4f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4v4f
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4v4f
Deposition date deposition_date2003-12-08
Structure title titleThe structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats
Keywords keywordsRNA BINDING PROTEIN, TRANSCRIPTION ATTENUATION, RNA-BINDING PROTEIN, TRP RNA; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier48.29
Radius of gyration Rg (electron density) rg_electron47.46
Forward intensity I(0) i02129180000.00
Molecular weight molecular_weight365140.0 kDa
Excluded volume excluded_volume449660 ų
Envelope volume envelope_volume598540 ų
Hydration-shell volume shell_volume103060 ų
Envelope diameter envelope_diameter151.6
Shell Rg shell_rg53.65
Envelope Rg envelope_rg46.04
Shape Rg shape_rg47.47
Total Rg total_rg47.67
Total atoms total_atoms25720
Residues n_residues3155
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 dmax152.7
Rg (real space) rg_real48.17
Rg uncertainty (real space) rg_real_error1.01
I(0) (real space) i0_real2.1290e+09
I(0) uncertainty (real space) i0_real_error4.0540e+07
Rg (reciprocal space) rg_reciprocal48.29
I(0) (reciprocal space) i0_reciprocal2129000000.0000
Solution quality estimate total_estimate0.8468
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.5
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha199900000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.420

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (3)

9. Files and Curves (10)