SAXSdb — 3gcm

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

Polyribonucleotide nucleotidyltransferase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ribonuclease E × 3 （A7ZKI9） CITRATE ANION × 8 MAGNESIUM ION × 3 GUANOSINE-5'-MONOPHOSPHATE × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNP_ECO24
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–549； UniProt 1–549 Author chain B； PDBConstruct 1–549； UniProt 1–549 Author chain C； PDBConstruct 1–549； UniProt 1–549

Ribonuclease E

OrganismNot specified

UniProt A7ZKI9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Polyribonucleotide nucleotidyltransferase × 3 （A7ZS61） CITRATE ANION × 8 MAGNESIUM ION × 3 GUANOSINE-5'-MONOPHOSPHATE × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A7ZKI9_ECO24
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–41； UniProt 1021–1061 Author chain E； PDBConstruct 1–41； UniProt 1021–1061 Author chain F； PDBConstruct 1–41； UniProt 1021–1061

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	3gcm
Deposition date deposition_date	2009-02-22
Structure title title	Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E
Keywords keywords	Protein-RNA complex, Cytoplasm, Nucleotidyltransferase, RNA-binding, Transferase, Hydrolase, transferase - protein binding COMPLEX; transferase / protein binding
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.

3gcm__assembly_1__model_1

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

Download this curve (.dat)

3gcm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gcm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.54 Å
Rg (electron density)	35.62 Å
Total Rg	36.26 Å
Atom count	12952
Residues	1694
Excluded volume	229570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gcm__assembly_1__model_1`	hexameric （6）	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	Polyribonucleotide nucleotidyltransferase
Molecular weight formula_weight	59657.8 kDa
EC 编号 ec_number	2.7.7.8
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	13916

MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAPRGDIS

Entity 2 Entity 2 polymer

Description description	Ribonuclease E
Molecular weight formula_weight	4340.7 kDa
EC 编号 ec_number	3.1.4.-
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

EAPRHSDWQRPTFAFEGKGAAGGHTATHHASAAPARPQPVE

Entity 3 Entity 3 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	884

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	3gcmA01
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	3gcmA02
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	3gcmA03
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	3gcmB01
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	3gcmB02
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	3gcmB03
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	3gcmC01
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	3gcmC02
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	3gcmC03
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	176.335 Å
Unit-cell length b length_b	176.335 Å
Unit-cell length c length_c	189.628 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1691
R_work r_work	0.1664
R_free r_free	0.2207

Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E

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

Polyribonucleotide nucleotidyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Ribonuclease E

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

3gcm__assembly_1__model_1

3gcm__assembly_1__model_1 | I(q)

3gcm__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

Entity 2 Entity 2 polymer

Polymer 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) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E

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

Polyribonucleotide nucleotidyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease E

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

3gcm__assembly_1__model_1

3gcm__assembly_1__model_1 | I(q)

3gcm__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

Entity 2 Entity 2 polymer

Polymer 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) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)