SAXSdb — 4hg9

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

Basic phospholipase A2 B

OrganismNot specified

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 17–138 Chain D； UniProt 17–138	Fragment：UNP residues 17-138	CA CALCIUM ION × 2 CIT CITRIC ACID × 2 G3P SN-GLYCEROL-3-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；287 K；18% MPEG5000, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.60 Å R-free 0.193
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 17–138 Chain C； UniProt 17–138	Fragment：UNP residues 17-138	CA CALCIUM ION × 2 G3P SN-GLYCEROL-3-PHOSPHATE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；287 K；18% MPEG5000, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.60 Å R-free 0.193

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 4HG9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4W BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS FOR ITS ASSOCIATION AND ANTICOAGULANT ACTIVITIES BY X-RAY CRYSTALLOGRAPHY Deposited 1998-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–122（122 aa） Chain B 1–122（122 aa） Chain C 1–122（122 aa） Chain D 1–122（122 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；THE PROTEIN SOLUTIONS CONTAINED 0.1M LI2SO4, 9% PEG 4K AND 0.3% N-OCTYL BETA- D-GLUCOPYRANOSIDE IN 0.01M TRIS-HCL BUFFER(PH 8.5) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 18% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17DEG.C.	Resolution 2.60 Å R-free 0.286
1JIA STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION Deposited 1997-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C.	Resolution 2.13 Å R-free 0.255

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

View Construct and Data Evidence

UniProt name	PA2BB_GLOHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 17–138 Author chain B； PDBConstruct 1–122； UniProt 17–138 Author chain C； PDBConstruct 1–122； UniProt 17–138 Author chain D； PDBConstruct 1–122； UniProt 17–138

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	4hg9
Deposition date deposition_date	2012-10-07
Structure title title	Crystal structure of AhV_bPA, a basic PLA2 from Agkistrodon halys pallas venom
Keywords keywords	alpha-helix, glycerophospholipid, venom gland, HYDROLASE; 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	24.41 Å
Radius of gyration Rg (electron density) rg_electron	23.43 Å
Forward intensity I(0) i0	55842800.00
Molecular weight molecular_weight	55112.0 kDa
Excluded volume excluded_volume	67546 Å³
Envelope volume envelope_volume	80719 Å³
Hydration-shell volume shell_volume	28696 Å³
Envelope diameter envelope_diameter	83.0 Å
Shell Rg shell_rg	30.71 Å
Envelope Rg envelope_rg	23.43 Å
Shape Rg shape_rg	23.41 Å
Total Rg total_rg	24.29 Å
Total atoms total_atoms	3812
Residues n_residues	488
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	81.1 Å
Rg (real space) rg_real	24.28 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	5.5840e+07
I(0) uncertainty (real space) i0_real_error	7.8140e+05
Rg (reciprocal space) rg_reciprocal	24.31 Å
I(0) (reciprocal space) i0_reciprocal	55840000.0000
Solution quality estimate total_estimate	0.8761
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.293
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8916000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.960

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Basic phospholipase A2 B
Molecular weight formula_weight	13938.1 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4257

HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKDGDIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SN-GLYCEROL-3-PHOSPHATE
Molecular weight formula_weight	172.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	393

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4hg9a_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

Domain ID domain_id	d4hg9b_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

Domain ID domain_id	d4hg9c_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

Domain ID domain_id	d4hg9d_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (4 domains)

Domain ID domain_id	4hg9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

Domain ID domain_id	4hg9B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

Domain ID domain_id	4hg9C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

Domain ID domain_id	4hg9D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

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8. Citations (1)

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Unit-cell length a length_a	98.953 Å
Unit-cell length b length_b	53.959 Å
Unit-cell length c length_c	108.433 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.000 Å
R factor r_factor	0.1726
R_work r_work	0.1709
R_free r_free	0.1927

fit	/app/data/saxs_computation/hg/4hg9/4hg9.fit
pddf	/app/data/pr_computation/hg/4hg9/4hg9.pr.out
profile	/app/data/saxs_computation/hg/4hg9/4hg9.dat

Crystal structure of AhV_bPA, a basic PLA2 from Agkistrodon halys pallas venom

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

Basic phospholipase A2 B

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