1dbo
CRYSTAL STRUCTURE OF CHONDROITINASE B
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。
Assembly Composition of the Current Entry
| Assembly | Oligomeric State | 实体与Construct证据 | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Other combination Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 2 PDB declaration: monomeric | Entity 1：CHONDROITINASE B × 1 Entity 2：;4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose ; × 1 Entity 3：4-deoxy-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose × 1 缺少 UniProt 身份时不显示参考序列区间 | Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.7；293 K；PEG8000, 2-METHYL-2,4-PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.7, VAPOR DIFFUSION, temperature 293K | Resolution 1.70 Å R-free 0.217 |
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
P(r) Distance Distribution P(r) Distribution
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 1dbo |
| Deposition date deposition_date | 1999-11-03 |
| Structure title title | CRYSTAL STRUCTURE OF CHONDROITINASE B |
| Keywords keywords | ACTIVE SITE, BETA-ELIMINATION, DEMATAN SULFATE, LYASE; LYASE |
| Experimental Method method | X-RAY DIFFRACTION |
3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)
| Radius of gyration Rg (Guinier) rg_guinier | 23.45 Å |
| Radius of gyration Rg (electron density) rg_electron | 22.76 Å |
| Forward intensity I(0) i0 | 50794600.00 |
| Molecular weight molecular_weight | 55272.0 kDa |
| Excluded volume excluded_volume | 69084 ų |
| Envelope volume envelope_volume | 78888 ų |
| Hydration-shell volume shell_volume | 28298 ų |
| Envelope diameter envelope_diameter | 80.2 Å |
| Shell Rg shell_rg | 30.56 Å |
| Envelope Rg envelope_rg | 23.15 Å |
| Shape Rg shape_rg | 22.71 Å |
| Total Rg total_rg | 23.81 Å |
| Total atoms total_atoms | 3885 |
| Residues n_residues | 480 |
| 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/ų |
| Shell contrast contrast_shell | 0.0300 e/ų |
| CRYSOL version crysol_version | 4.1.3 |
4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)
| Maximum dimension Dmax dmax | 77.9 Å |
| Rg (real space) rg_real | 23.39 Å |
| Rg uncertainty (real space) rg_real_error | 0.40 Å |
| I(0) (real space) i0_real | 5.0790e+07 |
| I(0) uncertainty (real space) i0_real_error | 7.1810e+05 |
| Rg (reciprocal space) rg_reciprocal | 23.41 Å |
| I(0) (reciprocal space) i0_reciprocal | 50800000.0000 |
| Solution quality estimate total_estimate | 0.8765 |
| Solution quality rating solution_quality | GOOD a GOOD solution |
| P(r) peaks n_peaks | 1 |
| Primary peak position r_peak_primary | 27.6 Å |
| Skewness Skewness skewness | 0.348 |
| Kurtosis Kurtosis kurtosis | -0.199 |
| Angular range angular_range | — – 0.3400 Å−1 |
| Current regularization parameter α current_alpha | 0.0001 |
| Highest regularization parameter α highest_alpha | 12150000.0000 |
| Real-space data points n_real_points | 66 |
| GNOM version gnom_version | 4.1.3 |
| Quality Criteria quality_criteria | AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994 |
5. Crystallography and Experiment 5. Crystallography & Experiment
6. Entities and Polymers Entities & Polymers (4)
7. Fold Classification (SCOP + CATH) 2 domains
SCOP 2.08 (1 domains)
| Domain ID domain_id | d1dboa_ |
| Class class | b — All beta proteins |
| Fold Fold fold | b.80 — Single-stranded right-handed beta-helix |
| Superfamily Superfamily superfamily | b.80.1 — Pectin lyase-like |
| Family Family family | b.80.1.4 — Chondroitinase B |
CATH v4.4 (1 domains)
| Domain ID domain_id | 1dboA00 |
| Class class | 2 — Mainly Beta |
| Architecture architecture | 160 — 3 Solenoid |
| Topology topology | 20 — Pectate Lyase C-like |
| Homologous superfamily homologous superfamily | 10 — Single-stranded right-handed beta-helix, Pectin lyase-like |