SAXSdb — 3dt9

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

Brain Platelet-activating factor acetylhydrolase IB subunit alpha

Bos taurus

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 1–232	Mutation：C55S	GD7 (1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Ammonium sulfate, Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.228

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 3DT9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BWP PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE Deposited 1998-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Mutation：L48A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.10 Å R-free 0.252
1BWQ PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE Deposited 1998-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Mutation：L194A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 2.30 Å R-free 0.274
1BWR PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE Deposited 1998-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Mutation：T103S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；pH 6.8	Resolution 2.40 Å R-free 0.264
1ES9 X-RAY CRYSTAL STRUCTURE OF R22K MUTANT OF THE MAMMALIAN BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES (PAF-AH) Deposited 2000-04-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Mutation：R22K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；1.6M Ammonium sulphate, 100mM sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 1.30 Å R-free 0.217
1FXW CRYSTAL STRUCTURE OF THE RECOMBINANT ALPHA1/ALPHA2 CATALYTIC HETERODIMER OF BOVINE BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB. Deposited 2000-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；17% PEG-MME 2000, 100 mM Na acetate, pH 6.4, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.275
1WAB PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE Deposited 1996-10-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
3DT6 Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Paraoxon Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–232（232 aa）	Mutation：C55S	DEP DIETHYL PHOSPHONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.206
3DT8 Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Sarin Deposited 2008-07-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–232（232 aa）	Mutation：C55S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.85 Å R-free 0.231

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA1B3_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 1–232

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dt9
Deposition date deposition_date	2008-07-14
Structure title title	Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Soman
Keywords keywords	;PLATELET ACTIVATING FACTOR ACETYLHYDROLASE, PAF-AH IB, ALPHA-1 SUBUNIT, LIS1, GROUP VIII PHOSPHOLIPASE A2, 26 kDa, SOMAN, Cytoplasm, Hydrolase, Lipid degradation, PLATELET FACTOR ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.85 Å
Radius of gyration Rg (electron density) rg_electron	16.40 Å
Forward intensity I(0) i0	10401300.00
Molecular weight molecular_weight	23695.0 kDa
Excluded volume excluded_volume	29588 Å³
Envelope volume envelope_volume	33380 Å³
Hydration-shell volume shell_volume	16852 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	22.72 Å
Envelope Rg envelope_rg	16.70 Å
Shape Rg shape_rg	16.41 Å
Total Rg total_rg	17.38 Å
Total atoms total_atoms	1675
Residues n_residues	212
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/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	56.4 Å
Rg (real space) rg_real	17.70 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.0400e+07
I(0) uncertainty (real space) i0_real_error	1.2210e+05
Rg (reciprocal space) rg_reciprocal	17.72 Å
I(0) (reciprocal space) i0_reciprocal	10400000.0000
Solution quality estimate total_estimate	0.7118
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2059000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 0.227; Positv: 1.000; Valcen: 0.984; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Brain Platelet-activating factor acetylhydrolase IB subunit alpha
Molecular weight formula_weight	25887.3 kDa
EC 编号 ec_number	3.1.1.47
Mutation mutation	C55S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1755

MSGDENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQSEIWRELFSPLHALNFGIGGDSTQHVLWRLENGELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLLRLLTQDQGQGGAPLPEPSP

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	bovine,cow,domestic cattle,domestic cow
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3dt9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

CATH v4.4 (1 domains)

Domain ID domain_id	3dt9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

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8. Citations (2)

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Unit-cell length a length_a	81.356 Å
Unit-cell length b length_b	81.356 Å
Unit-cell length c length_c	72.969 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2112
R_work r_work	0.2103
R_free r_free	0.2283

fit	/app/data/saxs_computation/dt/3dt9/3dt9.fit
pddf	/app/data/pr_computation/dt/3dt9/3dt9.pr.out
profile	/app/data/saxs_computation/dt/3dt9/3dt9.dat

Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Soman

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

Brain Platelet-activating factor acetylhydrolase IB subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction