SAXSdb — 1cjy

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

PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)

Homo sapiens

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 1–749	Not recorded	CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 2.50 Å R-free 0.298
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–749	Not recorded	CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 2.50 Å R-free 0.298

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 1CJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCI C2 DOMAIN OF CYTOSOLIC PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-04-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–138（138 aa） Fragment：C2 DOMAIN	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.1；308 K；Ionic strength (raw mmCIF value) 0.0；Pressure 1 NMR sample composition 20 MM TRIS, 0.5MM CACL2	Resolution not provided
1RLW CALCIUM-PHOSPHOLIPID BINDING DOMAIN FROM CYTOSOLIC PHOSPHOLIPASE A2 Deposited 1997-10-28	Different construct 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 17–141（125 aa） Fragment：C2 DOMAIN, RESIDUES 17 - 141 FROM CPLA2	Mutation：Y16S, C139A, C141S	CD CADMIUM ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；5-10MG/ML PROTEIN, 5MM CACL2, 1M SODIUM ACETATE, 0.1M HEPES (PH 7.5), 50MM CDSO4	Resolution 2.40 Å R-free 0.273

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

View Construct and Data Evidence

UniProt name	PA24A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–749； UniProt 1–749 Author chain B； PDBConstruct 1–749； UniProt 1–749

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	1cjy
Deposition date deposition_date	1999-04-20
Structure title title	HUMAN CYTOSOLIC PHOSPHOLIPASE A2
Keywords keywords	PHOSPHOLIPASE, LIPID-BINDING, 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	73.29 Å
Radius of gyration Rg (electron density) rg_electron	73.64 Å
Forward intensity I(0) i0	245436000.00
Molecular weight molecular_weight	137150.0 kDa
Excluded volume excluded_volume	172930 Å³
Envelope volume envelope_volume	293370 Å³
Hydration-shell volume shell_volume	32729 Å³
Envelope diameter envelope_diameter	221.1 Å
Shell Rg shell_rg	80.37 Å
Envelope Rg envelope_rg	67.99 Å
Shape Rg shape_rg	73.63 Å
Total Rg total_rg	73.77 Å
Total atoms total_atoms	9648
Residues n_residues	1247
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	234.3 Å
Rg (real space) rg_real	73.85 Å
Rg uncertainty (real space) rg_real_error	2.55 Å
I(0) (real space) i0_real	2.4540e+08
I(0) uncertainty (real space) i0_real_error	5.9010e+06
Rg (reciprocal space) rg_reciprocal	70.55 Å
I(0) (reciprocal space) i0_reciprocal	243700000.0000
Solution quality estimate total_estimate	0.5433
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.115
Kurtosis Kurtosis kurtosis	-1.531
Angular range angular_range	— – 0.1050 Å⁻¹
Current regularization parameter α current_alpha	0.0011
Highest regularization parameter α highest_alpha	4282000.0000
Real-space data points n_real_points	22
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.060; Smooth: 0.000

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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	PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
Molecular weight formula_weight	85309.7 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9706

MSFIDPYQHIIVEHQYSHKFTVVVLRATKVTKGAFGDMLDTPDPYVELFISTTPDSRKRTRHFNNDINPVWNETFEFILDPNQENVLEITLMDANYVMDETLGTATFTVSSMKVGEKKEVPFIFNQVTEMVLEMSLEVCSCPDLRFSMALCDQEKTFRQQRKEHIRESMKKLLGPKNSEGLHSARDVPVVAILGSGGGFRAMVGFSGVMKALYESGILDCATYVAGLSGSTWYMSTLYSHPDFPEKGPEEINEELMKNVSHNPLLLLTPQKVKRYVESLWKKKSSGQPVTFTDIFGMLIGETLIHNRMNTTLSSLKEKVNTAQCPLPLFTCLHVKPDVSELMFADWVEFSPYEIGMAKYGTFMAPDLFGSKFFMGTVVKKYEENPLHFLMGVWGSAFSILFNRVLGVSGSQSRGSTMEEELENITTKHIVSNDSSDSDDESHEPKGTENEDAGSDYQSDNQASWIHRMIMALVSDSALFNTREGRAGKVHNFMLGLNLNTSYPLSPLSDFATQDSFDDDELDAAVADPDEFERIYEPLDVKSKKIHVVDSGLTFNLPYPLILRPQRGVDLIISFDFSARPSDSSPPFKELLLAEKWAKMNKLPFPKIDPYVFDREGLKECYVFKPKNPDMEKDCPTIIHFVLANINFRKYKAPGVPRETEEEKEIADFDIFDDPESPFSTFNFQYPNQAFKRLHDLMHFNTLNNIDVIKEAMVESIEYRRQNPSRCSVSLSNVEARRFFNKEFLSKPKA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

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	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cjya1
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.1 — PLC-like (P variant)

Domain ID domain_id	d1cjya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.19 — FabD/lysophospholipase-like
Superfamily Superfamily superfamily	c.19.1 — FabD/lysophospholipase-like
Family Family family	c.19.1.2 — Lysophospholipase

Domain ID domain_id	d1cjyb1
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.1 — PLC-like (P variant)

Domain ID domain_id	d1cjyb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.19 — FabD/lysophospholipase-like
Superfamily Superfamily superfamily	c.19.1 — FabD/lysophospholipase-like
Family Family family	c.19.1.2 — Lysophospholipase

CATH v4.4 (4 domains)

Domain ID domain_id	1cjyA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	1cjyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1090 — Cytosolic phospholipase A2 catalytic domain
Homologous superfamily homologous superfamily	10 — Cytosolic phospholipase A2 catalytic domain

Domain ID domain_id	1cjyB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	1cjyB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1090 — Cytosolic phospholipase A2 catalytic domain
Homologous superfamily homologous superfamily	10 — Cytosolic phospholipase A2 catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	153.590 Å
Unit-cell length b length_b	95.490 Å
Unit-cell length c length_c	139.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2980

fit	/app/data/saxs_computation/cj/1cjy/1cjy.fit
pddf	/app/data/pr_computation/cj/1cjy/1cjy.pr.out
profile	/app/data/saxs_computation/cj/1cjy/1cjy.dat

HUMAN CYTOSOLIC PHOSPHOLIPASE A2

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

PROTEIN (CYTOSOLIC 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