SAXSdb — 2dzy

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

Cysteine proteinase 1

Saccharomyces cerevisiae

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：N392A	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 2.57 Å R-free 0.253

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 2DZY	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
2DZZ Crystal structure of N392V 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：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 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 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 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 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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2dzy
Deposition date deposition_date	2006-09-30
Structure title title	Crystal structure of N392A mutant of yeast bleomycin hydrolase
Keywords keywords	bleomycin hydrolase, thiol protease, C1 protease, buried water, HYDROLASE; HYDROLASE
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	25.81 Å
Radius of gyration Rg (electron density) rg_electron	24.92 Å
Forward intensity I(0) i0	43663300.00
Molecular weight molecular_weight	52291.0 kDa
Excluded volume excluded_volume	65999 Å³
Envelope volume envelope_volume	84793 Å³
Hydration-shell volume shell_volume	28377 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	31.91 Å
Envelope Rg envelope_rg	25.96 Å
Shape Rg shape_rg	24.90 Å
Total Rg total_rg	25.81 Å
Total atoms total_atoms	3686
Residues n_residues	457
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	89.7 Å
Rg (real space) rg_real	25.82 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	4.3660e+07
I(0) uncertainty (real space) i0_real_error	5.9570e+05
Rg (reciprocal space) rg_reciprocal	25.82 Å
I(0) (reciprocal space) i0_reciprocal	43660000.0000
Solution quality estimate total_estimate	0.6897
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.383
Kurtosis Kurtosis kurtosis	-0.232
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7351000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 0.965; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Cysteine proteinase 1
Molecular weight formula_weight	52383.6 kDa
EC 编号 ec_number	3.4.22.40
Mutation mutation	N392A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3883

FQGAMSSSIDISKINSWNKEFQSDLTHQLATTVLKNYNADDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRCWLFAATNQLRLNVLSELNLKEFELSQAYLFFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQYSMFLNLVKKYGLIPKDLYGDLPYSTTASRKWNSLLTTKLREFAETLRTALKERSADDSIIVTLREQMQREIFRLMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIKSTPLEFASKYAKLDPSTPVSLINDPRHPYGKLIKIDRLGNVLGGDAVIYLNVDNETLSKLVVKRLQNNKAVFFGSHTPKFMDKKTGVMDIELWNYPAIGYNLPQQKASRIRYHESLMTHAMLITGCHVDETSKLPLRYRVEASWGKDSGKDGLYVMTQKYFEEYCFQIVVDINELPKELASKFTSGKEEPIVLPIWDPMGALA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dzya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d2dzya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2dzyA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	151.027 Å
Unit-cell length b length_b	151.027 Å
Unit-cell length c length_c	89.669 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	43.290 Å
R factor r_factor	0.2020
R_work r_work	0.1980
R_free r_free	0.2530

fit	/app/data/saxs_computation/dz/2dzy/2dzy.fit
pddf	/app/data/pr_computation/dz/2dzy/2dzy.pr.out
profile	/app/data/saxs_computation/dz/2dzy/2dzy.dat

Crystal structure of N392A mutant of yeast bleomycin hydrolase

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

Cysteine proteinase 1

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