SAXSdb — 1zpe

▼

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

Arginase 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	MANGANESE (II) ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARGI1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 6–319 Author chain B； PDBConstruct 1–314； UniProt 6–319 Author chain C； PDBConstruct 1–314； UniProt 6–319

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1zpe
Deposition date deposition_date	2005-05-16
Structure title title	Arginase I covalently modified with butylamine at Q19C
Keywords keywords	chemically modified enzyme, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1zpe__assembly_1__model_1

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

Download this curve (.dat)

1zpe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zpe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.52 Å
Rg (electron density)	18.45 Å
Total Rg	19.39 Å
Atom count	2393
Residues	313
Excluded volume	42981 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zpe__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zpe__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1zpe__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1zpe__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Arginase 1
Molecular weight formula_weight	33917.7 kDa
EC 编号 ec_number	3.5.3.1
Mutation mutation	C119A, C168A, C303A, H141A, Q19(BBC)
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7666

KPIEIIGAPFSKGCPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDHSMAIGSISGHARVHPDLAVIWVDAHTDINTPLTTSSGNLAGQPVAFLLKELKGKFPDVPGFSWVTPAISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSAFGTKREGNHKPETDYL

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	487

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1zpea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.1 — Arginase-like amidino hydrolases

Domain ID domain_id	d1zpeb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.1 — Arginase-like amidino hydrolases

Domain ID domain_id	d1zpec_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.1 — Arginase-like amidino hydrolases

CATH v4.4 (3 domains)

Domain ID domain_id	1zpeA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	10 — Ureohydrolase domain

Domain ID domain_id	1zpeB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	10 — Ureohydrolase domain

Domain ID domain_id	1zpeC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	10 — Ureohydrolase domain

▶

Unit-cell length a length_a	88.078 Å
Unit-cell length b length_b	88.078 Å
Unit-cell length c length_c	106.340 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	9

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	28.830 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2330

Arginase I covalently modified with butylamine at Q19C

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

Arginase 1

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

1zpe__assembly_1__model_1

1zpe__assembly_1__model_1 | I(q)

1zpe__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Arginase I covalently modified with butylamine at Q19C

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

Arginase 1

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

1zpe__assembly_1__model_1

1zpe__assembly_1__model_1 | I(q)

1zpe__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)