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9ect

Crystal Structure of the Gemella haemolysans Immunoglobulin A1 Protease Trypsin-Like Domain

Method: X-RAY DIFFRACTION Dmax: 83.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LPXTG-motif cell wall anchor domain protein

Gemella haemolysans

UniProt C5NYF3

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 661–873 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.2M KNO3, 25% (w/v) PEG3350 Resolution 1.75 Å R-free 0.242
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 661–873 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.2M KNO3, 25% (w/v) PEG3350 Resolution 1.75 Å R-free 0.242

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 9ECT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UVK G. haemolysans IgA1 protease Deposited 2022-05-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2178（2178 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7UVL IgA1 Protease with IgA1 substrate Deposited 2022-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 884–2178（1295 aa）
Mutation：A942E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å

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

View Construct and Data Evidence
UniProt name C5NYF3_9BACL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–215； UniProt 661–873 Author chain B； PDBConstruct 3–215； UniProt 661–873

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 9ect

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9ect
Deposition date deposition_date2024-11-15
Structure title titleCrystal Structure of the Gemella haemolysans Immunoglobulin A1 Protease Trypsin-Like Domain
Keywords keywordstrypsin-like fold, immunoglobulin A1 protease domain, secreted protein, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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_guinier25.51 Å
Radius of gyration Rg (electron density) rg_electron24.73 Å
Forward intensity I(0) i037559800.00
Molecular weight molecular_weight46215.0 kDa
Excluded volume excluded_volume57443 ų
Envelope volume envelope_volume70479 ų
Hydration-shell volume shell_volume24587 ų
Envelope diameter envelope_diameter85.4 Å
Shell Rg shell_rg30.97 Å
Envelope Rg envelope_rg24.91 Å
Shape Rg shape_rg24.70 Å
Total Rg total_rg25.54 Å
Total atoms total_atoms3267
Residues n_residues420
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 dmax83.5 Å
Rg (real space) rg_real25.61 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real3.7560e+07
I(0) uncertainty (real space) i0_real_error4.8270e+05
Rg (reciprocal space) rg_reciprocal25.58 Å
I(0) (reciprocal space) i0_reciprocal37560000.0000
Solution quality estimate total_estimate0.8737
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.461
Kurtosis Kurtosis kurtosis-0.375
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10830000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.915
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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)