SAXSdb — 2bx9

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

TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

BACILLUS SUBTILIS

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 1–53 Chain B； UniProt 1–53 Chain C； UniProt 1–53 Chain D； UniProt 1–53 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 Chain K； UniProt 1–53 Chain L； UniProt 1–53	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；CONDITIONS: 21-23 % (W/V) POLY(ETHYLENE) GLYCOL 5000 MONMETHYL ETHER; 0.1 M SODIUM CACODYLATE PH 6.5; 50 MM MAGNESIUM ACETATE CRYOSOLUTION: 16 % GLYCEROL (V/V) WITH HIGHER CONCENTRATION OF POLY(ETHYLENE) GLYCOL	Resolution 2.80 Å R-free 0.296

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.

Other PDB	Difference from Current Entry 2BX9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZP8 The Nature of the TRAP:Anti-TRAP complex Deposited 2008-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain E 1–53（53 aa） Chain F 1–53（53 aa） Chain G 1–53（53 aa） Chain H 1–53（53 aa） Chain I 1–53（53 aa） Chain J 1–53（53 aa）	Not recorded	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
2ZP9 The Nature of the TRAP:Anti-TRAP complex Deposited 2008-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain H 1–53（53 aa） Chain I 1–53（53 aa） Chain J 1–53（53 aa） Chain M 1–53（53 aa） Chain N 1–53（53 aa） Chain O 1–53（53 aa）	Not recorded	TRP TRYPTOPHAN × 12 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M succinate pH 7.0, 13-15% PEG 10000, 2% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.325
2ZP9 The Nature of the TRAP:Anti-TRAP complex Deposited 2008-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain C 1–53（53 aa） Chain D 1–53（53 aa） Chain E 1–53（53 aa）	Not recorded	TRP TRYPTOPHAN × 12 ZN ZINC ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M succinate pH 7.0, 13-15% PEG 10000, 2% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.325

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1–53 Author chain B； PDBConstruct 1–53； UniProt 1–53 Author chain C； PDBConstruct 1–53； UniProt 1–53 Author chain D； PDBConstruct 1–53； UniProt 1–53 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 Author chain K； PDBConstruct 1–53； UniProt 1–53 Author chain L； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bx9
Deposition date deposition_date	2005-07-26
Structure title title	Crystal structure of B.subtilis Anti-TRAP protein, an antagonist of TRAP-RNA interactions
Keywords keywords	TRANSCRIPTION REGULATION, ANTI-TRAP; TRANSCRIPTION REGULATION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	28.44 Å
Radius of gyration Rg (electron density) rg_electron	26.91 Å
Forward intensity I(0) i0	80459200.00
Molecular weight molecular_weight	68351.0 kDa
Excluded volume excluded_volume	84845 Å³
Envelope volume envelope_volume	108940 Å³
Hydration-shell volume shell_volume	33577 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	34.25 Å
Envelope Rg envelope_rg	27.07 Å
Shape Rg shape_rg	26.85 Å
Total Rg total_rg	27.85 Å
Total atoms total_atoms	4704
Residues n_residues	636
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	88.9 Å
Rg (real space) rg_real	28.21 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	8.0460e+07
I(0) uncertainty (real space) i0_real_error	1.0560e+06
Rg (reciprocal space) rg_reciprocal	28.28 Å
I(0) (reciprocal space) i0_reciprocal	80460000.0000
Solution quality estimate total_estimate	0.8861
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.7 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9357000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
Molecular weight formula_weight	5655.6 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	4847

MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK

来源 Source

来源生物 organism	BACILLUS SUBTILIS
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2bx9A00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9B00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9C00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9D00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9E00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9F00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9G00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9H00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9I00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9J00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9K00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bx9L00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	20 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	51.552 Å
Unit-cell length b length_b	60.125 Å
Unit-cell length c length_c	60.348 Å
Unit-cell angle α angle_alpha	113.99 °
Unit-cell angle β angle_beta	101.37 °
Unit-cell angle γ angle_gamma	100.50 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1970
R_work r_work	0.1920
R_free r_free	0.2960

fit	/app/data/saxs_computation/bx/2bx9/2bx9.fit
pddf	/app/data/pr_computation/bx/2bx9/2bx9.pr.out
profile	/app/data/saxs_computation/bx/2bx9/2bx9.dat

Crystal structure of B.subtilis Anti-TRAP protein, an antagonist of TRAP-RNA interactions

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

TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction