SAXSdb — 3tu8

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

Burkholderia Lethal Factor 1 (BLF1)

Burkholderia pseudomallei

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；26% PEG 3350, 0.2M Sodium bromide, 0.1M bis-tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.04 Å R-free 0.160

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 3TU8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TUA Crystal Structure of the Burkholderia Lethal Factor 1 (BLF1) C94S mutant Deposited 2011-09-16	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–211（210 aa）	Mutation：C94S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；26% PEG 3350, 0.2M Sodium bromide, 0.1M bis-tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.09 Å R-free 0.168
6RVU Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) Deposited 2019-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–211（211 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350	Resolution 0.99 Å R-free 0.147
7PPZ Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form A Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa）	Mutation：C94S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；0.1 M MES, 50 mM magnesium chloride, 10 % (w/v) 2-propanol, 5 % (w/v) PEG 4000	Resolution 2.52 Å R-free 0.276
7PQ0 Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form B Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa）	Mutation：C94S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；0.1 M HEPES, 4 % (w/v) PEG 6000	Resolution 3.00 Å R-free 0.230

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q63UP7_BURPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 2–211

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	3tu8
Deposition date deposition_date	2011-09-16
Structure title title	Crystal Structure of the Burkholderia Lethal Factor 1 (BLF1)
Keywords keywords	toxin, Unknown Function; UNKNOWN FUNCTION
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	18.03 Å
Radius of gyration Rg (electron density) rg_electron	16.63 Å
Forward intensity I(0) i0	10409600.00
Molecular weight molecular_weight	23303.0 kDa
Excluded volume excluded_volume	28806 Å³
Envelope volume envelope_volume	32257 Å³
Hydration-shell volume shell_volume	16301 Å³
Envelope diameter envelope_diameter	58.5 Å
Shell Rg shell_rg	22.68 Å
Envelope Rg envelope_rg	16.93 Å
Shape Rg shape_rg	16.61 Å
Total Rg total_rg	17.62 Å
Total atoms total_atoms	1640
Residues n_residues	209
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	58.1 Å
Rg (real space) rg_real	17.93 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.0410e+07
I(0) uncertainty (real space) i0_real_error	1.3780e+05
Rg (reciprocal space) rg_reciprocal	17.95 Å
I(0) (reciprocal space) i0_reciprocal	10410000.0000
Solution quality estimate total_estimate	0.8096
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.298
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1857000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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	Burkholderia Lethal Factor 1 (BLF1)
Molecular weight formula_weight	23244.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2131

PNSLEAQIRQAMKTGSTLTIEFDQALNQKSPGTLNVFLHPANGGVRIDLDSGNQGEPAKILWLPWKQGELQTLQPGSISTVDMLFFTYYLSGCKVFAGDGGPVWHIDAPVEANQFWRRMSSDEWMEDWEVGTDRQVAYLHRAGQSDSLWNLSAYLEGAAPSTYGRDNLGQAVVGGIVTGRQQMSLYQYATTSSGSSAWSPLTYTLQQRKQ

来源 Source

来源生物 organism	Burkholderia pseudomallei
NCBI Class编号 ncbi_taxonomy_id	28450
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	369

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8. Citations (2)

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Unit-cell length a length_a	37.034 Å
Unit-cell length b length_b	45.434 Å
Unit-cell length c length_c	111.405 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.040 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1290
R_work r_work	0.1290
R_free r_free	0.1600

fit	/app/data/saxs_computation/tu/3tu8/3tu8.fit
pddf	/app/data/pr_computation/tu/3tu8/3tu8.pr.out
profile	/app/data/saxs_computation/tu/3tu8/3tu8.dat

Crystal Structure of the Burkholderia Lethal Factor 1 (BLF1)

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

Burkholderia Lethal Factor 1 (BLF1)

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