SAXSdb — 1e3h

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

GUANOSINE PENTAPHOSPHATE SYNTHETASE

STREPTOMYCES ANTIBIOTICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 27 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53597
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–757； UniProt 1–740

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	1e3h
Deposition date deposition_date	2000-06-15
Structure title title	SeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme
Keywords keywords	POLYRIBONUCLEOTIDE TRANSFERASE, ATP:GTP DIPHOSPHOTRANSFERASE, RNA PROCESSING, RNA DEGRADATION; POLYRIBONUCLEOTIDE 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.

1e3h__assembly_1__model_1

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

Download this curve (.dat)

1e3h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e3h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.16 Å
Rg (electron density)	36.50 Å
Total Rg	36.90 Å
Atom count	13641
Residues	1755
Excluded volume	242650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e3h__assembly_1__model_1`	trimeric （3）	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	GUANOSINE PENTAPHOSPHATE SYNTHETASE
Molecular weight formula_weight	82163.3 kDa
EC 编号 ec_number	2.7.7.8, 2.7.6.5
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	4842

ASMTGGQQMGRGSGSEFMENETHYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLLPEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLIPVIEGEEAASDEKKDDAEQ

Source Source

Source organism organism	STREPTOMYCES ANTIBIOTICUS
NCBI taxonomy ID ncbi_taxonomy_id	1890
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	291

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1e3ha1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.9 — Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
Family Family family	a.4.9.1 — Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3

Domain ID domain_id	d1e3ha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.4 — Ribonuclease PH domain 1-like

Domain ID domain_id	d1e3ha3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.4 — Ribonuclease PH domain 1-like

Domain ID domain_id	d1e3ha4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.3 — Prokaryotic type KH domain (KH-domain type II)
Family Family family	d.52.3.1 — Prokaryotic type KH domain (KH-domain type II)

Domain ID domain_id	d1e3ha5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.101 — Ribonuclease PH domain 2-like
Superfamily Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
Family Family family	d.101.1.1 — Ribonuclease PH domain 2-like

Domain ID domain_id	d1e3ha6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.101 — Ribonuclease PH domain 2-like
Superfamily Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
Family Family family	d.101.1.1 — Ribonuclease PH domain 2-like

CATH v4.4 (3 domains)

Domain ID domain_id	1e3hA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	1e3hA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	400 — Polyribonucleotide nucleotidyltransferase, RNA-binding domain

Domain ID domain_id	1e3hA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

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Unit-cell length a length_a	133.610 Å
Unit-cell length b length_b	133.610 Å
Unit-cell length c length_c	344.470 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	38.990 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2260

SeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme

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

GUANOSINE PENTAPHOSPHATE SYNTHETASE

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

1e3h__assembly_1__model_1

1e3h__assembly_1__model_1 | I(q)

1e3h__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) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

SeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme

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

GUANOSINE PENTAPHOSPHATE SYNTHETASE

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

1e3h__assembly_1__model_1

1e3h__assembly_1__model_1 | I(q)

1e3h__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) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)