SAXSdb — 3ch0

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

Glycerophosphodiester phosphodiesterase

Cytophaga hutchinsonii ATCC 33406

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CITRIC ACID × 1 1,2-ETHANEDIOL × 16 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q11WD4_CYTH3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–272； UniProt 1–271

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	3ch0
Deposition date deposition_date	2008-03-06
Structure title title	Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
Keywords keywords	;YP_677622.1, glycerophosphoryl diester phosphodiesterase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Hydrolase ;; HYDROLASE
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.

3ch0__assembly_1__model_1

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

Download this curve (.dat)

3ch0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ch0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.13 Å
Rg (electron density)	18.04 Å
Total Rg	19.24 Å
Atom count	2231
Residues	265
Excluded volume	40283 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ch0__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Glycerophosphodiester phosphodiesterase
Molecular weight formula_weight	31104.6 kDa
EC 编号 ec_number	3.1.4.46
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	2775

GMIQVPASFDIQGHRGCRGLLPENTIAAFTKALLLGVTTLEFDLVISKDNRVVVSHDTFFHHEITMMVDGEDVTEANEKNFNLYAMNYADIKEIDVGMKTHPRFKSQKKVPAVKPLFRELIETAEKLSAKIQYNGEIKSTVEGDNIDHPNIALFCDLVVAEIKKAHITDRFTLQSFDVRALEYMHSQYPDIKLSYLVETKGTLKKQLEKLSFTPAVYSPDVTLVSKKDIDAAHKLGMRVIPWTVNTKEEIETLISLGVDGIITDYPDLFFEK

Source Source

Source organism organism	Cytophaga hutchinsonii ATCC 33406
NCBI taxonomy ID ncbi_taxonomy_id	269798
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	400

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ch0a1
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.1.18.0 — automated matches

Domain ID domain_id	d3ch0a2
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	3ch0A00
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	49.532 Å
Unit-cell length b length_b	61.211 Å
Unit-cell length c length_c	113.699 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	1.500 Å
Low-resolution limit resolution_low	29.553 Å
R factor r_factor	0.1600
R_work r_work	0.1580
R_free r_free	0.1890

Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

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

Glycerophosphodiester 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

3ch0__assembly_1__model_1

3ch0__assembly_1__model_1 | I(q)

3ch0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

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

Glycerophosphodiester 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

3ch0__assembly_1__model_1

3ch0__assembly_1__model_1 | I(q)

3ch0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)