SAXSdb — 1byl

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

PROTEIN (BLEOMYCIN RESISTANCE PROTEIN)

Streptoalloteichus hindustanus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–124	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；SEE REFERENCE 2, pH 6.0	Resolution 2.30 Å

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 1BYL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XRK Crystal structure of a mutant bleomycin binding protein from Streptoalloteichus hindustanus displaying increased thermostability Deposited 2004-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–124（124 aa） Chain B 1–124（124 aa）	Mutation：G18E, D32V, L63Q, G98V Mutation：G18E, D32V, L63Q, G98V	SO4 SULFATE ION × 3 BLM BLEOMYCIN A2 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.194
2ZHP Crystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative Deposited 2008-02-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–124（124 aa） Chain B 1–124（124 aa）	Not recorded	BY6 [(2S,3R,4R,5S,6S)-2-[(3R,4R,5R,6R)-2-[(1R,2S)-2-[[6-amino-2-[(1S)-3-amino-1-[(2,3-diamino-3-oxopropyl)amino]-3-oxopropyl]-5-methylpyrimidine-4-carbonyl]amino]-3-[[(2S,3R,4R)-5-[[(2R,3S)-1-[2-[4-[4-[3-[4-(3-aminopropylamino)butylamino]propylcarbamoyl]-1,3-thiazol-2-yl]-1,3-thiazol-2-yl]ethylamino]-3-hydroxy-1-oxobutan-2-yl]amino]-3-hydroxy-4-methyl-5-oxopentan-2-yl]amino]-1-(3H-imidazol-4-yl)-3-oxopropoxy]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl] carbamate × 2 CU COPPER (II) ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG550mme, zinc sulfate, sodium chloride, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.60 Å R-free 0.216

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

View Construct and Data Evidence

UniProt name	BLE_STRHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–125； UniProt 1–124

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	1byl
Deposition date deposition_date	1998-10-17
Structure title title	BLEOMYCIN RESISTANCE PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS
Keywords keywords	ANTIBIOTIC RESISTANCE, BLEOMYCIN, DRUG SEQUESTERING, CHAIN SWAPPING, ANTIBIOTIC; ANTIBIOTIC
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	16.11 Å
Radius of gyration Rg (electron density) rg_electron	14.90 Å
Forward intensity I(0) i0	3750930.00
Molecular weight molecular_weight	13542.0 kDa
Excluded volume excluded_volume	16875 Å³
Envelope volume envelope_volume	20149 Å³
Hydration-shell volume shell_volume	11935 Å³
Envelope diameter envelope_diameter	60.0 Å
Shell Rg shell_rg	20.31 Å
Envelope Rg envelope_rg	15.73 Å
Shape Rg shape_rg	14.85 Å
Total Rg total_rg	16.19 Å
Total atoms total_atoms	959
Residues n_residues	122
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	58.8 Å
Rg (real space) rg_real	16.09 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	3.7510e+06
I(0) uncertainty (real space) i0_real_error	4.9160e+04
Rg (reciprocal space) rg_reciprocal	16.09 Å
I(0) (reciprocal space) i0_reciprocal	3751000.0000
Solution quality estimate total_estimate	0.7476
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.390
Kurtosis Kurtosis kurtosis	0.141
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	609500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1byla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.2 — Antibiotic resistance proteins

CATH v4.4 (1 domains)

Domain ID domain_id	1bylA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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8. Citations (4)

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Unit-cell length a length_a	48.400 Å
Unit-cell length b length_b	48.400 Å
Unit-cell length c length_c	111.500 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1760
R_work r_work	0.1760
R_free r_free	—

Description description	PROTEIN (BLEOMYCIN RESISTANCE PROTEIN)
Molecular weight formula_weight	13953.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1021

BLEOMYCIN RESISTANCE PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS

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

PROTEIN (BLEOMYCIN RESISTANCE 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Streptoalloteichus hindustanus
NCBI Class编号 ncbi_taxonomy_id	2017
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

fit	/app/data/saxs_computation/by/1byl/1byl.fit
pddf	/app/data/pr_computation/by/1byl/1byl.pr.out
profile	/app/data/saxs_computation/by/1byl/1byl.dat