9yd8

Crystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum

Method: X-RAY DIFFRACTION Dmax: 74.5 Å Quality: EXCELLENT

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

Phospholipase D

Arcanobacterium haemolyticum

UniProt Q59121

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 31–309 Not recorded GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;0.01 M nickel(II) chloride hexahydrate, 0.1 M Tris pH 7.5, and 20% w/v polyethylene glycol monomethyl ether 2,000 Resolution 2.45 Å R-free 0.299
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 31–309 Not recorded GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;0.01 M nickel(II) chloride hexahydrate, 0.1 M Tris pH 7.5, and 20% w/v polyethylene glycol monomethyl ether 2,000 Resolution 2.45 Å R-free 0.299

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 PLD_ARCHD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 18–296; UniProt 31–309 Author chain B; PDBConstruct 18–296; UniProt 31–309

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 9yd8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yd8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yd8
Deposition date deposition_date2025-09-22
Structure title titleCrystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum
Keywords keywordssphingomyelinase D, hydrolase, Arcanobacterium haemolyticum, thermostability, phospholipase D, TOXIN; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.65
Radius of gyration Rg (electron density) rg_electron23.40
Forward intensity I(0) i066925200.00
Molecular weight molecular_weight62242.0 kDa
Excluded volume excluded_volume77133 ų
Envelope volume envelope_volume89357 ų
Hydration-shell volume shell_volume30969 ų
Envelope diameter envelope_diameter76.5
Shell Rg shell_rg31.24
Envelope Rg envelope_rg23.35
Shape Rg shape_rg23.35
Total Rg total_rg24.35
Total atoms total_atoms4395
Residues n_residues547
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 dmax74.5
Rg (real space) rg_real24.51
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real6.6930e+07
I(0) uncertainty (real space) i0_real_error9.4060e+05
Rg (reciprocal space) rg_reciprocal24.54
I(0) (reciprocal space) i0_reciprocal66930000.0000
Solution quality estimate total_estimate0.9060
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.439
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12350000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)