SAXSdb — 2o0v

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

Pectate lyase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid ; × 1 CALCIUM ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEL_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–399； UniProt 22–420

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	2o0v
Deposition date deposition_date	2006-11-28
Structure title title	Pectate lyase bound to hexasaccharide compound III
Keywords keywords	Michaelis complex with compound III, 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.

2o0v__assembly_1__model_1

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

Download this curve (.dat)

2o0v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o0v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.44 Å
Rg (electron density)	20.56 Å
Total Rg	21.42 Å
Atom count	3124
Residues	399
Excluded volume	54370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o0v__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 (4)

Entity 1 Entity 1 polymer

Description description	Pectate lyase
Molecular weight formula_weight	43359.1 kDa
EC 编号 ec_number	4.2.2.2
Mutation mutation	R279A
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	3755

ADLGHQTLGSNDGWGAYSTGTTGGSKASSSNVYTVSNRNQLVSALGKETNTTPKIIYIKGTIDMNVDDNLKPLGLNDYKDPEYDLDKYLKAYDPSTWGKKEPSGTQEEARARSQKNQKARVMVDIPANTTIVGSGTNAKVVGGNFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKNIVQAAPRVRFGQVHVYNNYYEGSTSSSSYPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTISVFSGGTALYDSGTLLNGTQINASAANGLSSSVGWTPSLHGSIDASANVKSNVINQAGAGKLN

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	;alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid ;
Molecular weight formula_weight	898.6 kDa
Source method src_method	man
Copy count entity_count	1

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	631

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2o0va_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.1 — Pectate lyase-like

CATH v4.4 (1 domains)

Domain ID domain_id	2o0vA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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Unit-cell length a length_a	50.712 Å
Unit-cell length b length_b	68.694 Å
Unit-cell length c length_c	59.444 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.02 °
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	1.900 Å
Low-resolution limit resolution_low	45.310 Å
R factor r_factor	0.1560
R_work r_work	0.1537
R_free r_free	0.1991

Pectate lyase bound to hexasaccharide compound III

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

Pectate lyase

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

2o0v__assembly_1__model_1

2o0v__assembly_1__model_1 | I(q)

2o0v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Pectate lyase bound to hexasaccharide compound III

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

Pectate lyase

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

2o0v__assembly_1__model_1

2o0v__assembly_1__model_1 | I(q)

2o0v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)