SAXSdb — 1qmh

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

;RNA 3'-TERMINAL PHOSPHATE CYCLASE ;

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CITRIC ACID × 2 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RTCA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–339； UniProt 2–338 Author chain B； PDBConstruct 3–339； UniProt 2–338

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	1qmh
Deposition date deposition_date	1999-09-28
Structure title title	Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
Keywords keywords	;2'3'CYCLIC PHOSPHATE RNA, LIGASE ;; LIGASE
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.

1qmh__assembly_1__model_1

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

Download this curve (.dat)

1qmh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qmh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.67 Å
Rg (electron density)	26.50 Å
Total Rg	27.28 Å
Atom count	5006
Residues	669
Excluded volume	89253 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qmh__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 (4)

Entity 1 Entity 1 polymer

Description description	;RNA 3'-TERMINAL PHOSPHATE CYCLASE ;
Molecular weight formula_weight	37014.2 kDa
EC 编号 ec_number	6.5.1.4
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	5430

MVKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIEGSHHHHHH

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL
Molecular weight formula_weight	170.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1qmha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
Family Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

Domain ID domain_id	d1qmha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

Domain ID domain_id	d1qmhb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.2 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain
Family Family family	c.47.2.1 — RNA 3'-terminal phosphate cyclase, RPTC, insert domain

Domain ID domain_id	d1qmhb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.1 — RNA 3'-terminal phosphate cyclase, RPTC

CATH v4.4 (4 domains)

Domain ID domain_id	1qmhA01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

Domain ID domain_id	1qmhA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

Domain ID domain_id	1qmhB01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase domain

Domain ID domain_id	1qmhB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	20 — RNA 3'-terminal phosphate cyclase, insert domain

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Unit-cell length a length_a	125.800 Å
Unit-cell length b length_b	133.500 Å
Unit-cell length c length_c	51.000 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2070
R_work r_work	0.2040
R_free r_free	0.2760

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology

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

;RNA 3'-TERMINAL PHOSPHATE CYCLASE ;

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

1qmh__assembly_1__model_1

1qmh__assembly_1__model_1 | I(q)

1qmh__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology

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

;RNA 3'-TERMINAL PHOSPHATE CYCLASE ;

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

1qmh__assembly_1__model_1

1qmh__assembly_1__model_1 | I(q)

1qmh__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)