SAXSdb — 2zkm

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2

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 X； UniProt 1–799	Fragment：residues 1-799 (PH-C2 domains)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；16%(v/v) isopropanol, 2%(v/v) dioxane, 100mM Tris , pH 8.5, VAPOR DIFFUSION, sitting drop, temperature 291K	Resolution 1.62 Å R-free 0.213

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 2ZKM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FJU Activated Rac1 bound to its effector phospholipase C beta 2 Deposited 2006-01-03	Different construct 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 1–799（799 aa） Fragment：residues 1-799	Not recorded	MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；8% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.20 Å R-free 0.226

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLCB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–799； UniProt 1–799

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	2zkm
Deposition date deposition_date	2008-03-26
Structure title title	Crystal Structure of Phospholipase C Beta 2
Keywords keywords	;phospholipase C, phosphoinositide phospholipase, PLC-Beta-2, Calcium, Coiled coil, Hydrolase, Lipid degradation, Metal-binding, Transducer ;; 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	28.51 Å
Radius of gyration Rg (electron density) rg_electron	27.59 Å
Forward intensity I(0) i0	101567000.00
Molecular weight molecular_weight	81153.0 kDa
Excluded volume excluded_volume	102380 Å³
Envelope volume envelope_volume	123320 Å³
Hydration-shell volume shell_volume	36317 Å³
Envelope diameter envelope_diameter	89.6 Å
Shell Rg shell_rg	35.71 Å
Envelope Rg envelope_rg	27.84 Å
Shape Rg shape_rg	27.59 Å
Total Rg total_rg	28.39 Å
Total atoms total_atoms	5705
Residues n_residues	708
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	88.4 Å
Rg (real space) rg_real	28.40 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.0160e+08
I(0) uncertainty (real space) i0_real_error	1.2600e+06
Rg (reciprocal space) rg_reciprocal	28.44 Å
I(0) (reciprocal space) i0_reciprocal	101600000.0000
Solution quality estimate total_estimate	0.9059
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.231
Kurtosis Kurtosis kurtosis	-0.516
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	21930000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2
Molecular weight formula_weight	91033.9 kDa
EC 编号 ec_number	3.1.4.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	6397

MSLLNPVLLPPKVKAYLSQGERFIKWDDETTVASPVILRVDPKGYYLYWTYQSKEMEFLDITSIRDTRFGKFAKMPKSQKLRDVFNMDFPDNSFLLKTLTVVSGPDMVDLTFHNFVSYKENVGKAWAEDVLALVKHPLTANASRSTFLDKILVKLKMQLNSEGKIPVKNFFQMFPADRKRVEAALSACHLPKGKNDAINPEDFPEPVYKSFLMSLCPRPEIDEIFTSYHAKAKPYMTKEHLTKFINQKQRDSRLNSLLFPPARPDQVQGLIDKYEPSGINAQRGQLSPEGMVWFLCGPENSVLAQDKLLLHHDMTQPLNHYFINSSHNTYLTAGQFSGLSSAEMYRQVLLSGCRCVELDCWKGKPPDEEPIITHGFTMTTDIFFKEAIEAIAESAFKTSPYPIILSFENHVDSPRQQAKMAEYCRTIFGDMLLTEPLEKFPLKPGVPLPSPEDLRGKILIKNKKNQFSGPTSSSKDTGGEAEGSSPPSAPAVWAGEEGTELEEEEVEEEEEEESGNLDEEEIKKMQSDEGTAGLEVTAYEEMSSLVNYIQPTKFVSFEFSAQKNRSYVISSFTELKAYDLLSKASVQFVDYNKRQMSRIYPKGTRMDSSNYMPQMFWNAGCQMVALNFQTMDLPMQQNMAVFEFNGQSGYLLKHEFMRRPDKQFNPFSVDRIDVVVATTLSITVISGQFLSERSVRTYVEVELFGLPGDPKRRYRTKLSPSTNSINPVWKEEPFVFEKILMPELASLRVAVMEEGNKFLGHRIIPINALNSGYHHLCLHSESNMPLTMPALFIFLEMKD

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	Spodoptera frugiperda

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	692

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2zkmx1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.7 — EF-hand modules in multidomain proteins

Domain ID domain_id	d2zkmx2
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	d2zkmx3
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

Domain ID domain_id	d2zkmx4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.18 — PLC-like phosphodiesterases
Family Family family	c.1.18.1 — Mammalian PLC

CATH v4.4 (4 domains)

Domain ID domain_id	2zkmX01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	2zkmX02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2zkmX03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

Domain ID domain_id	2zkmX04
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 (2)

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Unit-cell length a length_a	80.404 Å
Unit-cell length b length_b	86.379 Å
Unit-cell length c length_c	147.447 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	19.450 Å
R factor r_factor	0.1970
R_work r_work	0.1960
R_free r_free	0.2130

fit	/app/data/saxs_computation/zk/2zkm/2zkm.fit
pddf	/app/data/pr_computation/zk/2zkm/2zkm.pr.out
profile	/app/data/saxs_computation/zk/2zkm/2zkm.dat

Crystal Structure of Phospholipase C Beta 2

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2

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