2zp8

The Nature of the TRAP:Anti-TRAP complex

Method: X-RAY DIFFRACTION Dmax: 103.2 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 heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) 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 Not recorded Tryptophan RNA-binding attenuator protein-inhibitory protein × 18 (O31466) TRP TRYPTOPHAN × 12 ZN ZINC ION × 18 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;293 K;0.1M bicine pH 9.0, 10-13% PEG 10000, 2% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.268

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 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTRB_BACST
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

Tryptophan RNA-binding attenuator protein-inhibitory protein

Bacillus subtilis

UniProt O31466

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 heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain E; UniProt 1–53 Chain F; UniProt 1–53 Chain G; UniProt 1–53 Chain H; UniProt 1–53 Chain I; UniProt 1–53 Chain J; UniProt 1–53 Not recorded Transcription attenuation protein mtrB × 12 (Q9X6J6) TRP TRYPTOPHAN × 12 ZN ZINC ION × 18 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;293 K;0.1M bicine pH 9.0, 10-13% PEG 10000, 2% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.268

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RTPA_BACSU
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–53; UniProt 1–53 Author chain F; PDBConstruct 1–53; UniProt 1–53 Author chain G; PDBConstruct 1–53; UniProt 1–53 Author chain H; PDBConstruct 1–53; UniProt 1–53 Author chain I; PDBConstruct 1–53; UniProt 1–53 Author chain J; PDBConstruct 1–53; UniProt 1–53

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 2zp8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zp8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zp8
Deposition date deposition_date2008-07-08
Structure title titleThe Nature of the TRAP:Anti-TRAP complex
Keywords keywordsPROTEIN-PROTEIN COMPLEX, TRANSCRIPTION, RNA-binding, Transcription regulation, RNA BINDING PROTEIN-TRANSCRIPTION COMPLEX; RNA BINDING PROTEIN/TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.37
Radius of gyration Rg (electron density) rg_electron28.65
Forward intensity I(0) i071642100.00
Molecular weight molecular_weight65405.0 kDa
Excluded volume excluded_volume81540 ų
Envelope volume envelope_volume104490 ų
Hydration-shell volume shell_volume31415 ų
Envelope diameter envelope_diameter112.3
Shell Rg shell_rg34.61
Envelope Rg envelope_rg29.27
Shape Rg shape_rg28.55
Total Rg total_rg29.53
Total atoms total_atoms4559
Residues n_residues593
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 dmax103.2
Rg (real space) rg_real29.46
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real7.1640e+07
I(0) uncertainty (real space) i0_real_error1.1600e+06
Rg (reciprocal space) rg_reciprocal29.42
I(0) (reciprocal space) i0_reciprocal71640000.0000
Solution quality estimate total_estimate0.7850
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6
Skewness Skewness skewness0.453
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9793000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id2zp8A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zp8B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zp8C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zp8D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily50 — TRAP-like
Domain ID domain_id2zp8E00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10
Domain ID domain_id2zp8F00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10
Domain ID domain_id2zp8G00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10
Domain ID domain_id2zp8H00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10
Domain ID domain_id2zp8I00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10
Domain ID domain_id2zp8J00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)