SAXSdb — 6th5

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

Alr0975 protein

Nostoc sp. PCC 7120

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 × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8YY76_NOSS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–218； UniProt 25–242 Author chain B； PDBConstruct 1–218； UniProt 25–242

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	6th5
Deposition date deposition_date	2019-11-18
Structure title title	Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975
Keywords keywords	Phytochelatin, heavy-metal detoxification, glutathione, gamma-glutamyl cysteine, TRANSFERASE; TRANSFERASE
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.

6th5__assembly_1__model_1

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

Download this curve (.dat)

6th5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6th5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.51 Å
Rg (electron density)	21.38 Å
Total Rg	22.28 Å
Atom count	6725
Residues	427
Excluded volume	60357 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6th5__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	Alr0975 protein
Molecular weight formula_weight	24643.9 kDa
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	7113

QTLTLSPNLIGFNSNEGEKLLLTSRSREDFFPLSMQFVTQVNQAYCGVASIIMVLNSLGINAPETAQYSPYRVFTQDNFFSNEKTKAVIAPEVVARQGMTLDELGRLIASYGVKVKVNHASDTNIEDFRKQVAENLKQDGNFVIVNYLRKEIGQERGGHISPLAAYNEQTDRFLIMDVSRYKYPPVWVKTTDLWKAMNTVDSVSQKTRGFVFVSKTQD

Source Source

Source organism organism	Nostoc sp. PCC 7120
NCBI taxonomy ID ncbi_taxonomy_id	103690
Host organism host_organism	Escherichia coli BL21(DE3)

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	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6th5a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.14 — Phytochelatin synthase

Domain ID domain_id	d6th5b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.14 — Phytochelatin synthase

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Unit-cell length a length_a	61.356 Å
Unit-cell length b length_b	46.670 Å
Unit-cell length c length_c	68.583 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	34.260 Å
R factor r_factor	0.2013
R_work r_work	0.1993
R_free r_free	0.2383

Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975

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

Alr0975 protein

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

6th5__assembly_1__model_1

6th5__assembly_1__model_1 | I(q)

6th5__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 (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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975

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

Alr0975 protein

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

6th5__assembly_1__model_1

6th5__assembly_1__model_1 | I(q)

6th5__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 (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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)