SAXSdb — 1xrk

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

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 Chain B； UniProt 1–124	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

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 1XRK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYL BLEOMYCIN RESISTANCE PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS Deposited 1998-10-17	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）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；SEE REFERENCE 2, pH 6.0	Resolution 2.30 Å
2ZHP Crystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative Deposited 2008-02-06	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 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； 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	1xrk
Deposition date deposition_date	2004-10-15
Structure title title	Crystal structure of a mutant bleomycin binding protein from Streptoalloteichus hindustanus displaying increased thermostability
Keywords keywords	Arm exchange, Ligand binding protein, Thermostable mutant, ANTIBIOTIC INHIBITOR; ANTIBIOTIC INHIBITOR
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	18.93 Å
Radius of gyration Rg (electron density) rg_electron	17.45 Å
Forward intensity I(0) i0	16406300.00
Molecular weight molecular_weight	29428.0 kDa
Excluded volume excluded_volume	36231 Å³
Envelope volume envelope_volume	40515 Å³
Hydration-shell volume shell_volume	19049 Å³
Envelope diameter envelope_diameter	59.9 Å
Shell Rg shell_rg	24.07 Å
Envelope Rg envelope_rg	17.68 Å
Shape Rg shape_rg	17.41 Å
Total Rg total_rg	18.50 Å
Total atoms total_atoms	2075
Residues n_residues	241
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	59.9 Å
Rg (real space) rg_real	18.81 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.6410e+07
I(0) uncertainty (real space) i0_real_error	1.5860e+05
Rg (reciprocal space) rg_reciprocal	18.83 Å
I(0) (reciprocal space) i0_reciprocal	16410000.0000
Solution quality estimate total_estimate	0.8934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3417000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Bleomycin resistance protein
Molecular weight formula_weight	13919.4 kDa
Mutation mutation	G18E, D32V, L63Q, G98V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2368

MAKLTSAVPVLTARDVAEAVEFWTDRLGFSRVFVEDDFAGVVRDDVTLFISAVQDQVVPDNTQAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIVEQPWGREFALRDPAGNCVHFVAEEQD

来源 Source

来源生物 organism	Streptoalloteichus hindustanus
NCBI Class编号 ncbi_taxonomy_id	2017
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	BLEOMYCIN A2
Molecular weight formula_weight	1416.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xrka_
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

Domain ID domain_id	d1xrkb_
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 (2 domains)

Domain ID domain_id	1xrkA00
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

Domain ID domain_id	1xrkB00
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 (1)

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Unit-cell length a length_a	43.983 Å
Unit-cell length b length_b	66.617 Å
Unit-cell length c length_c	47.179 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1751
R_work r_work	0.1740
R_free r_free	0.1943

fit	/app/data/saxs_computation/xr/1xrk/1xrk.fit
pddf	/app/data/pr_computation/xr/1xrk/1xrk.pr.out
profile	/app/data/saxs_computation/xr/1xrk/1xrk.dat

Crystal structure of a mutant bleomycin binding protein from Streptoalloteichus hindustanus displaying increased thermostability

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

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