1utd

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

Method: X-RAY DIFFRACTION Dmax: 101.3 Å Quality: EXCELLENT

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 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: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 2.10 Å R-free 0.228
2 Protein–RNA Homooligomer Protein × 11 RNA 11 PDB declaration: 22-meric(22) 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 5'-R(*GP*UP*UP*UP*GP*AP)-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 2.10 Å R-free 0.228

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_BACST
Isoform
PDB entities 2
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 1utd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1utd
Deposition date deposition_date2003-12-08
Structure title titleThe structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats
Keywords keywordsRNA BINDING PROTEIN, TRANSCRIPTION REGULATION, RNA-BINDING, TRP RNA TRANSCRIPTION ATTENUATION, 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_guinier35.91
Radius of gyration Rg (electron density) rg_electron34.49
Forward intensity I(0) i0602116000.00
Molecular weight molecular_weight186810.0 kDa
Excluded volume excluded_volume228880 ų
Envelope volume envelope_volume291820 ų
Hydration-shell volume shell_volume66136 ų
Envelope diameter envelope_diameter102.0
Shell Rg shell_rg44.56
Envelope Rg envelope_rg33.56
Shape Rg shape_rg34.44
Total Rg total_rg35.27
Total atoms total_atoms13141
Residues n_residues1593
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 dmax101.3
Rg (real space) rg_real35.56
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real6.0210e+08
I(0) uncertainty (real space) i0_real_error9.2160e+06
Rg (reciprocal space) rg_reciprocal35.78
I(0) (reciprocal space) i0_reciprocal602200000.0000
Solution quality estimate total_estimate0.9062
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.7
Skewness Skewness skewness-0.107
Kurtosis Kurtosis kurtosis-0.636
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha700300000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.968

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 44 domains

SCOP 2.08 (22 domains)

Domain ID domain_idd1utda_
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_idd1utdb_
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_idd1utdc_
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_idd1utdd_
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_idd1utde_
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_idd1utdf_
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_idd1utdg_
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_idd1utdh_
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_idd1utdi_
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_idd1utdj_
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_idd1utdk_
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_idd1utdl_
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_idd1utdm_
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_idd1utdn_
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_idd1utdo_
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_idd1utdp_
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_idd1utdq_
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_idd1utdr_
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_idd1utds_
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_idd1utdt_
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_idd1utdu_
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_idd1utdv_
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 (22 domains)

Domain ID domain_id1utdA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdM00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdO00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdP00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdR00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdS00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdT00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdU00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id1utdV00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like

8. Citations (3)

9. Files and Curves (10)