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1gcb

GAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL)

Method: X-RAY DIFFRACTION Dmax: 84.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GAL6 HG (EMTS) DERIVATIVE

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 Not recorded SO4 SULFATE ION × 18 HG MERCURY (II) ION × 24 GOL GLYCEROL × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 Å R-free 0.274

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 1GCB 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
2DZY Crystal structure of N392A mutant of yeast bleomycin hydrolase Deposited 2006-09-30 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：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 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：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 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：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 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：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 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：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
2E03 Crystal structure of NQ67E mutant of yeast bleomycin hydrolase Deposited 2006-10-01 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：Q67E 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 2.13 Å R-free 0.256
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 1–454； 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 1gcb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gcb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gcb
Deposition date deposition_date1995-07-18
Structure title titleGAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL)
Keywords keywords;DNA-BINDING, PEPTIDASE, CYSTEINE PROTEASE, REGULATORY FACTOR, BLEOMYCIN HYDROLASE, RING PROTEIN, DNA-BINDING PROTEIN, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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_guinier25.20 Å
Radius of gyration Rg (electron density) rg_electron24.48 Å
Forward intensity I(0) i047641300.00
Molecular weight molecular_weight52995.0 kDa
Excluded volume excluded_volume65866 ų
Envelope volume envelope_volume82307 ų
Hydration-shell volume shell_volume27982 ų
Envelope diameter envelope_diameter90.1 Å
Shell Rg shell_rg31.63 Å
Envelope Rg envelope_rg25.34 Å
Shape Rg shape_rg24.52 Å
Total Rg total_rg25.13 Å
Total atoms total_atoms3678
Residues n_residues452
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 dmax84.8 Å
Rg (real space) rg_real25.20 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real4.7640e+07
I(0) uncertainty (real space) i0_real_error7.0430e+05
Rg (reciprocal space) rg_reciprocal25.20 Å
I(0) (reciprocal space) i0_reciprocal47640000.0000
Solution quality estimate total_estimate0.8796
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.246
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5850000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.979
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1gcba_
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

CATH v4.4 (1 domains)

Domain ID domain_id1gcbA01
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 (2)

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9. Files and Curves (10)