SAXSdb — 1t6m

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

1-phosphatidylinositol phosphodiesterase

Bacillus thuringiensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLC_BACTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–299； UniProt 32–329 Author chain B； PDBConstruct 2–299； UniProt 32–329

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	1t6m
Deposition date deposition_date	2004-05-06
Structure title title	X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.
Keywords keywords	PI-PLC, lyase; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1t6m__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1t6m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t6m__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.87 Å
Rg (electron density)	29.35 Å
Total Rg	29.96 Å
Atom count	4838
Residues	592
Excluded volume	85696 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t6m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	1-phosphatidylinositol phosphodiesterase
Molecular weight formula_weight	34638.6 kDa
EC 编号 ec_number	4.6.1.13
Mutation mutation	R70D
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	5066

MASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIDGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLIKE

Source Source

Source organism organism	Bacillus thuringiensis
NCBI taxonomy ID ncbi_taxonomy_id	1428
Host organism host_organism	Escherichia coli

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	228

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1t6ma_
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.1.18.2 — Bacterial PLC

Domain ID domain_id	d1t6mb_
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.1.18.2 — Bacterial PLC

CATH v4.4 (2 domains)

Domain ID domain_id	1t6mA00
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	1t6mB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

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Unit-cell length a length_a	91.221 Å
Unit-cell length b length_b	147.725 Å
Unit-cell length c length_c	96.562 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.107 Å
Low-resolution limit resolution_low	43.300 Å
R factor r_factor	0.2233
R_work r_work	0.2233
R_free r_free	0.2397

X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.

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

1-phosphatidylinositol phosphodiesterase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1t6m__assembly_1__model_1

1t6m__assembly_1__model_1 | I(q)

1t6m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.

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

1-phosphatidylinositol phosphodiesterase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1t6m__assembly_1__model_1

1t6m__assembly_1__model_1 | I(q)

1t6m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)