SAXSdb — 1ywp

▼

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1

Rattus norvegicus

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 790–851	Fragment：Phospholipase C-gamma1 Mutation：C5S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 4000, sodium acetate, Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.60 Å R-free 0.188

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 1YWP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y0M Crystal structure of of the SH3 domain of phospholipase C Gamma-1 Deposited 2004-11-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 791–851（61 aa） Fragment：SH3 domain: sequence database residues 791-851	Mutation：C794S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.177
1YWO Phospholipase Cgamma1 SH3 in complex with a SLP-76 motif Deposited 2005-02-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 790–851（62 aa）	Mutation：C5S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.81 Å R-free 0.221
2FJL Solution Structure of the Split PH domain in Phospholipase C-gamma1 Deposited 2006-01-03	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 489–547（59 aa） Fragment：the Split PH2 domain, residuse 1-35 and 112-148 Chain A 851–933（83 aa） Fragment：the Split PH2 domain, residuse 1-35 and 112-148	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Pressure ambient NMR sample composition 1.0mM of the PHN-PHC tandem U-15N; 50mM potassium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 100% D2O \| 100% D2O NMR sample composition 1.0mM of the PHN-PHC tandem; 50mM potassium phosphate; 100% D2O \| 100% D2O	Resolution not provided
3GQI Crystal Structure of activated receptor tyrosine kinase in complex with substrates Deposited 2009-03-24	Different construct 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 B 545–770（226 aa） Fragment：tandem SH2 domains	Not recorded	DVT DECAVANADATE × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEg 8000, taurine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.289
4K44 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；100 mM MES, 200 mM ammonium acetate, 25% (w/v) PEG 4.000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.223
4K44 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；100 mM MES, 200 mM ammonium acetate, 25% (w/v) PEG 4.000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.223
4K45 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain Chain B 770–787（18 aa） Fragment：residues 770 to 787 of PLC-gamma1	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；pH 6；293 K；100 mM MES, 200 mM ammonium acetate, 35% (w/v) PEG 4,000, microseeding, pH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 1.50 Å R-free 0.198
5EG3 Crystal Structure of the Activated FGF Receptor 2 (FGFR2) Kinase Domain in complex with the cSH2 domain of Phospholipase C gamma (PLCgamma) Deposited 2015-10-26	Different construct 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 B 661–773（113 aa） Fragment：UNP residues 661-773	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；25 mM HEPES (pH 7.5), PEG20000 (12% 18%) and 2% (w/v) Benzamidine hydrochloride	Resolution 2.61 Å R-free 0.237
6PBC Structural basis for the activation of PLC-gamma isozymes by phosphorylation and cancer-associated mutations Deposited 2019-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 791–1215（425 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% w/v PEG 3,350, 50 mM di-sodium tartrate, 5% v/v glycerol	Resolution 2.46 Å R-free 0.245
7Z3J Structure of crystallisable rat Phospholipase C gamma 1 in complex with inositol 1,4,5-trisphosphate Deposited 2022-03-02	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 20–790（771 aa） Chain A 791–1215（425 aa）	Not recorded	CA CALCIUM ION × 2 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；18.7 % PEG 3350, 0.1 M CBTP	Resolution 2.00 Å R-free 0.256
9QB7 Structure of rat Phospholipase C gamma 1 mutant S345F Deposited 2025-02-28	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 1–765（765 aa） Chain A 791–1290（500 aa）	Mutation：S345F Mutation：S345F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；18.7 % PEG 3350, 0.1 M CBTP, PH 7.0	Resolution 2.56 Å R-free 0.233

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLCG1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–64； UniProt 790–851

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ywp
Deposition date deposition_date	2005-02-18
Structure title title	Phospholipase Cgamma1 SH3
Keywords keywords	SH3, Phospholipase C-gamma1, SLP-76, SH2 domain-containing leukocyte phosphoprotein of 76 kD, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	12.43 Å
Radius of gyration Rg (electron density) rg_electron	11.02 Å
Forward intensity I(0) i0	1153710.00
Molecular weight molecular_weight	7217.0 kDa
Excluded volume excluded_volume	9091 Å³
Envelope volume envelope_volume	10268 Å³
Hydration-shell volume shell_volume	8145 Å³
Envelope diameter envelope_diameter	40.1 Å
Shell Rg shell_rg	16.49 Å
Envelope Rg envelope_rg	11.69 Å
Shape Rg shape_rg	10.95 Å
Total Rg total_rg	12.73 Å
Total atoms total_atoms	512
Residues n_residues	62
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

▼

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

Maximum dimension Dmax dmax	42.6 Å
Rg (real space) rg_real	12.38 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.1540e+06
I(0) uncertainty (real space) i0_real_error	1.2860e+04
Rg (reciprocal space) rg_reciprocal	12.38 Å
I(0) (reciprocal space) i0_reciprocal	1154000.0000
Solution quality estimate total_estimate	0.8505
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.057
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	366200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.958

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ywpa1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1ywpa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1ywpA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

▶

8. Citations (1)

▶

Unit-cell length a length_a	28.967 Å
Unit-cell length b length_b	31.280 Å
Unit-cell length c length_c	29.778 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.490 Å
R factor r_factor	0.1446
R_work r_work	0.1424
R_free r_free	0.1877

Description description	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1
Molecular weight formula_weight	7414.3 kDa
EC 编号 ec_number	3.1.4.11
Mutation mutation	C5S
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	632

Phospholipase Cgamma1 SH3

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

fit	/app/data/saxs_computation/yw/1ywp/1ywp.fit
pddf	/app/data/pr_computation/yw/1ywp/1ywp.pr.out
profile	/app/data/saxs_computation/yw/1ywp/1ywp.dat