3zzs

Engineered 12-subunit Bacillus stearothermophilus trp RNA-binding attenuation protein (TRAP)

Method: X-RAY DIFFRACTION Dmax: 91.5 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 × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 5–69 Chain B; UniProt 5–69 Chain C; UniProt 5–69 Fragment:RESIDUES 5-69 TRP TRYPTOPHAN × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.49 Å R-free 0.182
2 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain D; UniProt 5–69 Chain E; UniProt 5–69 Chain F; UniProt 5–69 Fragment:RESIDUES 5-69 TRP TRYPTOPHAN × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.49 Å R-free 0.182
3 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain G; UniProt 5–69 Chain H; UniProt 5–69 Chain I; UniProt 5–69 Fragment:RESIDUES 5-69 TRP TRYPTOPHAN × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.49 Å R-free 0.182

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 47 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 1–65; UniProt 5–69 Author chain B; PDBConstruct 1–65; UniProt 5–69 Author chain C; PDBConstruct 1–65; UniProt 5–69 Author chain D; PDBConstruct 1–65; UniProt 5–69 Author chain E; PDBConstruct 1–65; UniProt 5–69 Author chain F; PDBConstruct 1–65; UniProt 5–69 Author chain G; PDBConstruct 1–65; UniProt 5–69 Author chain H; PDBConstruct 1–65; UniProt 5–69 Author chain I; PDBConstruct 1–65; UniProt 5–69

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 3zzs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zzs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zzs
Deposition date deposition_date2011-09-02
Structure title titleEngineered 12-subunit Bacillus stearothermophilus trp RNA-binding attenuation protein (TRAP)
Keywords keywordsTRANSCRIPTION, TRANSCRIPTION REGULATION, PROTEIN ENGINEERING; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.18
Radius of gyration Rg (electron density) rg_electron28.65
Forward intensity I(0) i071886900.00
Molecular weight molecular_weight66527.0 kDa
Excluded volume excluded_volume83488 ų
Envelope volume envelope_volume107770 ų
Hydration-shell volume shell_volume31487 ų
Envelope diameter envelope_diameter98.8
Shell Rg shell_rg35.67
Envelope Rg envelope_rg28.23
Shape Rg shape_rg28.62
Total Rg total_rg29.44
Total atoms total_atoms4706
Residues n_residues585
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 dmax91.5
Rg (real space) rg_real29.11
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real7.1890e+07
I(0) uncertainty (real space) i0_real_error1.0590e+06
Rg (reciprocal space) rg_reciprocal29.15
I(0) (reciprocal space) i0_reciprocal71890000.0000
Solution quality estimate total_estimate0.9053
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.0
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.574
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26090000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd3zzsa_
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_idd3zzsb_
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_idd3zzsc_
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_idd3zzsd_
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_idd3zzse_
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_idd3zzsf_
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_idd3zzsg_
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_idd3zzsh_
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_idd3zzsi_
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 (9 domains)

Domain ID domain_id3zzsA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id3zzsI00
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)