SAXSdb — 1r76

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

pectate lyase

Azospirillum irakense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 CHLORIDE ION × 1 ISOPROPYL ALCOHOL × 1 GLYCEROL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X592_AZOIR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–408； UniProt 25–432

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	1r76
Deposition date deposition_date	2003-10-20
Structure title title	Structure of a pectate lyase from Azospirillum irakense
Keywords keywords	a-helical structure, 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.

1r76__assembly_1__model_1

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

Download this curve (.dat)

1r76__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r76__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.43 Å
Rg (electron density)	21.64 Å
Total Rg	22.57 Å
Atom count	2993
Residues	384
Excluded volume	52808 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r76__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 (6)

Entity 1 Entity 1 polymer

Description description	pectate lyase
Molecular weight formula_weight	44551.7 kDa
EC 编号 ec_number	4.2.2.2
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	3247

AVIGMNEAASALTPSRVSSLPDTQRAAWQEYLARSEAQLSRDKASLAAELAPGQPLPPPPAEGKGADTMPLDKPAAWYTSKAARHVADVIVSFQTPAGGWGKNQPRDGALRLPGQHYTGENVAKVKSGSNDLDAARDRDWHYVGTIDNDATVTEIRFLAQVVSQLAPEEAAPYRDAALKGIEYLLASQFPNGGWPQVWPLEGGYHDAITYNDDALVHVAELLSDIAAGRDGFGFVPPAIRTRALEATNAAIHCIVETQVVQDGKRLGWGQQHDALTLRPTSARNFEPAALSSTESARILLFLMEIEAPSDAVKQAIRGGVAWLNTSVIRDRAWVKSDQGYQLVTEQGAKPLWSRFYSLDGNKPVFGDRDKTIHDDVMGISQERRTGYAWYTTSPQKALSAFTKWEKRS

Source Source

Source organism organism	Azospirillum irakense
NCBI taxonomy ID ncbi_taxonomy_id	34011
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1r76a_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.5 — Family 10 polysaccharide lyase
Family Family family	a.102.5.1 — Family 10 polysaccharide lyase

CATH v4.4 (1 domains)

Domain ID domain_id	1r76A00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	85.374 Å
Unit-cell length b length_b	85.374 Å
Unit-cell length c length_c	231.317 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	21.750 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2620

Structure of a pectate lyase from Azospirillum irakense

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

1r76__assembly_1__model_1

1r76__assembly_1__model_1 | I(q)

1r76__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of a pectate lyase from Azospirillum irakense

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

1r76__assembly_1__model_1

1r76__assembly_1__model_1 | I(q)

1r76__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)