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2e03

Crystal structure of NQ67E mutant of yeast bleomycin hydrolase

Method: X-RAY DIFFRACTION Dmax: 90.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine proteinase 1

Saccharomyces cerevisiae

UniProt Q01532

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–454 Mutation：Q67E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K, 100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.13 Å R-free 0.256

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 2E03 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A6R GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A Deposited 1998-02-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：HIS6-TEV-TAG, S2A, C73A SO4 SULFATE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE AND PEG 4K., pH 9.0
Resolution 2.05 Å R-free 0.257
1GCB GAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL) Deposited 1995-07-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Not recorded SO4 SULFATE ION × 18 HG MERCURY (II) ION × 24 GOL GLYCEROL × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.274
2DZY Crystal structure of N392A mutant of yeast bleomycin hydrolase Deposited 2006-09-30 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：N392A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K,100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.57 Å R-free 0.253
2DZZ Crystal structure of N392V mutant of yeast bleomycin hydrolase Deposited 2006-09-30 Different mutation/modification Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：N392V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K, 100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.15 Å R-free 0.232
2E00 Crystal structure of N392L mutant of yeast bleomycin hydrolase Deposited 2006-10-01 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：N392L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K,100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.00 Å R-free 0.248
2E01 Crystal structure of H369A mutant of yeast bleomycin hydrolase Deposited 2006-10-01 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：H369A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K,100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.73 Å R-free 0.224
2E02 Crystal structure of H369L mutant of yeast bleomycin hydrolase Deposited 2006-10-01 Different mutation/modification Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Mutation：H369L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；14-20% PEG 4K, 100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.20 Å R-free 0.260
3GCB GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454 Deposited 1998-02-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 3–453（451 aa）
Mutation：HIS6-TEV-TAG, C73A, DEL(K454) SO4 SULFATE ION × 30 GOL GLYCEROL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE AND PEG MME 2K., pH 8.5
Resolution 1.87 Å R-free 0.217

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLH1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–457； UniProt 1–454

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 2e03

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2e03
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2e03
Deposition date deposition_date2006-10-01
Structure title titleCrystal structure of NQ67E mutant of yeast bleomycin hydrolase
Keywords keywordsbleomycin hydrolase, thiol protease, C1 proteas, HYDROLASE; HYDROLASE
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_guinier26.13 Å
Radius of gyration Rg (electron density) rg_electron25.23 Å
Forward intensity I(0) i041266000.00
Molecular weight molecular_weight51044.0 kDa
Excluded volume excluded_volume64506 ų
Envelope volume envelope_volume83530 ų
Hydration-shell volume shell_volume27820 ų
Envelope diameter envelope_diameter95.2 Å
Shell Rg shell_rg32.02 Å
Envelope Rg envelope_rg26.11 Å
Shape Rg shape_rg25.21 Å
Total Rg total_rg26.09 Å
Total atoms total_atoms3599
Residues n_residues444
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 dmax90.8 Å
Rg (real space) rg_real26.13 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real4.1270e+07
I(0) uncertainty (real space) i0_real_error6.4340e+05
Rg (reciprocal space) rg_reciprocal26.13 Å
I(0) (reciprocal space) i0_reciprocal41270000.0000
Solution quality estimate total_estimate0.8735
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8 Å
Skewness Skewness skewness0.365
Kurtosis Kurtosis kurtosis-0.249
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6999000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.976
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2e03a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like
Domain ID domain_idd2e03a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2e03A01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
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8. Citations (1)

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9. Files and Curves (10)