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9xlc

Crystal structure of the GH16 carrageenase SfGH16 from Saccharicrinis fermentans

Method: X-RAY DIFFRACTION Dmax: 61.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Kappa-carrageenase

Saccharicrinis fermentans DSM 9555 = JCM 21142

UniProt W7YHV7

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 21–284 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；290 K；0.1M Bis-Tris pH5.5, 25%PEG3350, 0.2M ammonium acetate Resolution 2.00 Å R-free 0.241

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 9XLC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9XKT Crystal structure of the complex of the GH16 carrageenase SfGH16 from Saccharicrinis fermentans with an oligotetrasaccharide of iota-carrageenan Deposited 2025-11-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–284（264 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M Sodium citrate tribasic dihydrate pH 5.60, 20% v/v 2-Propanol
Resolution 1.44 Å R-free 0.175
9XL7 Crystal structure of the complex of the GH16 carrageenase SfGH16 from Saccharicrinis fermentans with an oligotetrasaccharide of kappa-carrageenan Deposited 2025-11-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–284（264 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350
Resolution 1.70 Å R-free 0.204

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name W7YHV7_9BACT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–284； UniProt 21–284

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 9xlc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xlc
Deposition date deposition_date2025-11-07
最后修订 last_revision2026-03-11
Structure title titleCrystal structure of the GH16 carrageenase SfGH16 from Saccharicrinis fermentans
Keywords keywordsglycoside hydrolase, GH16 family, carrageenase, apo, 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_guinier18.99 Å
Radius of gyration Rg (electron density) rg_electron17.85 Å
Forward intensity I(0) i015517300.00
Molecular weight molecular_weight29782.0 kDa
Excluded volume excluded_volume37239 ų
Envelope volume envelope_volume41579 ų
Hydration-shell volume shell_volume19192 ų
Envelope diameter envelope_diameter62.4 Å
Shell Rg shell_rg24.48 Å
Envelope Rg envelope_rg18.16 Å
Shape Rg shape_rg17.82 Å
Total Rg total_rg18.90 Å
Total atoms total_atoms2111
Residues n_residues261
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 dmax61.3 Å
Rg (real space) rg_real18.87 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real1.5520e+07
I(0) uncertainty (real space) i0_real_error1.6690e+05
Rg (reciprocal space) rg_reciprocal18.89 Å
I(0) (reciprocal space) i0_reciprocal15520000.0000
Solution quality estimate total_estimate0.8873
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7 Å
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.374
Angular range angular_range— – 0.4200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5857000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999
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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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8. Citations (1)

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9. Files and Curves (10)