SAXSdb — 1c1j

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

BASIC PHOSPHOLIPASE A2

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 1–122 Chain D； UniProt 1–122	Not recorded	BOG octyl beta-D-glucopyranoside × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, n-octyl beta-D-glycopyranoside, CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 2.80 Å R-free 0.282
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–122 Chain C； UniProt 1–122	Not recorded	BOG octyl beta-D-glucopyranoside × 1 CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, n-octyl beta-D-glycopyranoside, CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 2.80 Å R-free 0.282

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	PA21B_AGKHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 1–122 Author chain B； PDBConstruct 1–112； UniProt 1–122 Author chain C； PDBConstruct 1–112； UniProt 1–122 Author chain D； PDBConstruct 1–112； UniProt 1–122

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	1c1j
Deposition date deposition_date	1999-07-22
Structure title title	STRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTRONDON HALYS PALLAS AT 2.8 ANGSTROMS RESOLUTION
Keywords keywords	VENOM, PHOSPHOLIPASE A2, CADMIUM, CATALYTIC MECHANISM, 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	24.47 Å
Radius of gyration Rg (electron density) rg_electron	23.62 Å
Forward intensity I(0) i0	58940200.00
Molecular weight molecular_weight	56880.0 kDa
Excluded volume excluded_volume	69765 Å³
Envelope volume envelope_volume	82907 Å³
Hydration-shell volume shell_volume	29142 Å³
Envelope diameter envelope_diameter	85.0 Å
Shell Rg shell_rg	30.99 Å
Envelope Rg envelope_rg	23.71 Å
Shape Rg shape_rg	23.63 Å
Total Rg total_rg	24.39 Å
Total atoms total_atoms	3902
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	82.2 Å
Rg (real space) rg_real	24.34 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	5.8940e+07
I(0) uncertainty (real space) i0_real_error	8.0490e+05
Rg (reciprocal space) rg_reciprocal	24.37 Å
I(0) (reciprocal space) i0_reciprocal	58940000.0000
Solution quality estimate total_estimate	0.8712
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.6 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10070000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BASIC PHOSPHOLIPASE A2
Molecular weight formula_weight	13922.2 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	3949

HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKNATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC

Entity 2 Entity 2 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c1ja_
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	d1c1jb_
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	d1c1jc_
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	d1c1jd_
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	1c1jA00
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	1c1jB00
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	1c1jC00
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	1c1jD00
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 (2)

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Unit-cell length a length_a	100.180 Å
Unit-cell length b length_b	54.010 Å
Unit-cell length c length_c	108.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.59 °
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	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2820

fit	/app/data/saxs_computation/c1/1c1j/1c1j.fit
pddf	/app/data/pr_computation/c1/1c1j/1c1j.pr.out
profile	/app/data/saxs_computation/c1/1c1j/1c1j.dat

STRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTRONDON HALYS PALLAS AT 2.8 ANGSTROMS RESOLUTION

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

BASIC PHOSPHOLIPASE A2

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