9y4v

Crystal structure of a GH5_18 from Microbacterium oxydans DSM 20578

Method: X-RAY DIFFRACTION Dmax: 101.6 Å Quality: GOOD

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

Glycosyl hydrolase

Microbacterium oxydans

UniProt A0A3Q9J612

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 1–436 Chain B; UniProt 1–436 Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;20% (w/v) PEG 3350, 0.2 M MgCl2, 0.1 M Tris pH 8.5 Resolution 1.92 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A3Q9J612_9MICO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 22–457; UniProt 1–436 Author chain B; PDBConstruct 22–457; UniProt 1–436

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 9y4v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y4v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y4v
Deposition date deposition_date2025-09-03
Structure title titleCrystal structure of a GH5_18 from Microbacterium oxydans DSM 20578
Keywords keywordsglycoside hydrolase, N-glycan degradation, GH5, enzyme, CAZyme, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.31
Radius of gyration Rg (electron density) rg_electron30.75
Forward intensity I(0) i0129866000.00
Molecular weight molecular_weight89705.0 kDa
Excluded volume excluded_volume111540 ų
Envelope volume envelope_volume130650 ų
Hydration-shell volume shell_volume36355 ų
Envelope diameter envelope_diameter107.0
Shell Rg shell_rg36.92
Envelope Rg envelope_rg31.07
Shape Rg shape_rg30.71
Total Rg total_rg31.38
Total atoms total_atoms6348
Residues n_residues822
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax101.6
Rg (real space) rg_real31.49
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.2990e+08
I(0) uncertainty (real space) i0_real_error1.8650e+06
Rg (reciprocal space) rg_reciprocal31.41
I(0) (reciprocal space) i0_reciprocal129900000.0000
Solution quality estimate total_estimate0.8526
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48490000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.717

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)