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2zhp

Crystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative

Method: X-RAY DIFFRACTION Dmax: 67.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bleomycin resistance protein

Streptoalloteichus hindustanus

UniProt P17493

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 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

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 2ZHP 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
1XRK Crystal structure of a mutant bleomycin binding protein from Streptoalloteichus hindustanus displaying increased thermostability Deposited 2004-10-15 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2zhp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2zhp
Deposition date deposition_date2008-02-06
Structure title titleCrystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative
Keywords keywordsANTIBIOTIC RESISTANCE, bleomycin, Ligand binding protein, ANTIBIOTIC INHIBITOR; ANTIBIOTIC INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.58 Å
Radius of gyration Rg (electron density) rg_electron17.18 Å
Forward intensity I(0) i015332100.00
Molecular weight molecular_weight28380.0 kDa
Excluded volume excluded_volume34891 ų
Envelope volume envelope_volume38779 ų
Hydration-shell volume shell_volume18546 ų
Envelope diameter envelope_diameter58.2 Å
Shell Rg shell_rg23.72 Å
Envelope Rg envelope_rg17.38 Å
Shape Rg shape_rg17.16 Å
Total Rg total_rg18.16 Å
Total atoms total_atoms1993
Residues n_residues231
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.9 Å
Rg (real space) rg_real18.45 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real1.5330e+07
I(0) uncertainty (real space) i0_real_error2.0910e+05
Rg (reciprocal space) rg_reciprocal18.47 Å
I(0) (reciprocal space) i0_reciprocal15330000.0000
Solution quality estimate total_estimate0.7515
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.132
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3546000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.591; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2zhpa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamilyd.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family familyd.32.1.2 — Antibiotic resistance proteins
Domain ID domain_idd2zhpb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamilyd.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family familyd.32.1.2 — Antibiotic resistance proteins

CATH v4.4 (2 domains)

Domain ID domain_id2zhpA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
Domain ID domain_id2zhpB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
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8. Citations (1)

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9. Files and Curves (10)