SAXSdb — 1rlw

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

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 17–141	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

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 1RLW	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 mutation/modification 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
1CJY HUMAN CYTOSOLIC PHOSPHOLIPASE A2 Deposited 1999-04-20	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 1–749（749 aa）	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
1CJY HUMAN CYTOSOLIC PHOSPHOLIPASE A2 Deposited 1999-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–749（749 aa）	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 other PDB entries and 3 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 2–126； UniProt 17–141

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	1rlw
Deposition date deposition_date	1997-10-28
Structure title title	CALCIUM-PHOSPHOLIPID BINDING DOMAIN FROM CYTOSOLIC PHOSPHOLIPASE A2
Keywords keywords	HYDROLASE, C2 DOMAIN, CALB DOMAIN; 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	16.48 Å
Radius of gyration Rg (electron density) rg_electron	15.32 Å
Forward intensity I(0) i0	4200960.00
Molecular weight molecular_weight	14549.0 kDa
Excluded volume excluded_volume	18073 Å³
Envelope volume envelope_volume	20271 Å³
Hydration-shell volume shell_volume	11810 Å³
Envelope diameter envelope_diameter	58.0 Å
Shell Rg shell_rg	20.48 Å
Envelope Rg envelope_rg	15.78 Å
Shape Rg shape_rg	15.21 Å
Total Rg total_rg	16.62 Å
Total atoms total_atoms	1005
Residues n_residues	126
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	58.1 Å
Rg (real space) rg_real	16.53 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	4.2010e+06
I(0) uncertainty (real space) i0_real_error	5.2320e+04
Rg (reciprocal space) rg_reciprocal	16.52 Å
I(0) (reciprocal space) i0_reciprocal	4201000.0000
Solution quality estimate total_estimate	0.8511
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.285
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	869000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.985

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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	PHOSPHOLIPASE A2
Molecular weight formula_weight	14299.2 kDa
EC 编号 ec_number	3.1.1.4
Mutation mutation	Y16S, C139A, C141S
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	1156

SSHKFTVVVLRATKVTKGAFGDMLDTPDPYVELFISTTPDSRKRTRHFNNDINPVWNETFEFILDPNQENVLEITLMDANYVMDETLGTATFTVSSMKVGEKKEVPFIFNQVTEMVLEMSLEVASS

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	151

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1rlwa_
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)

CATH v4.4 (1 domains)

Domain ID domain_id	1rlwA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (1)

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Unit-cell length a length_a	79.410 Å
Unit-cell length b length_b	79.410 Å
Unit-cell length c length_c	70.670 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	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2270
R_free r_free	0.2730

fit	/app/data/saxs_computation/rl/1rlw/1rlw.fit
pddf	/app/data/pr_computation/rl/1rlw/1rlw.pr.out
profile	/app/data/saxs_computation/rl/1rlw/1rlw.dat

CALCIUM-PHOSPHOLIPID BINDING DOMAIN FROM CYTOSOLIC PHOSPHOLIPASE A2

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

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