SAXSdb — 4dwr

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

tRNA-splicing ligase RtcB

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 MANGANESE (II) ION × 2 SULFATE ION × 8 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 MANGANESE (II) ION × 2 SULFATE ION × 6 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 MANGANESE (II) ION × 2 SULFATE ION × 7 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RTCB_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 1–97 Author chain A； PDBConstruct 98–481； UniProt 488–871 Author chain B； PDBConstruct 1–97； UniProt 1–97 Author chain B； PDBConstruct 98–481； UniProt 488–871 Author chain C； PDBConstruct 1–97； UniProt 1–97 Author chain C； PDBConstruct 98–481； UniProt 488–871

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	4dwr
Deposition date deposition_date	2012-02-26
Structure title title	RNA ligase RtcB/Mn2+ complex
Keywords keywords	RNA ligase, RtcB, Mn2+, 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.

4dwr__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4dwr__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dwr__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	22.25 Å
Rg (electron density)	21.40 Å
Total Rg	22.25 Å
Atom count	3827
Residues	481
Excluded volume	67832 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dwr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4dwr__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4dwr__assembly_3__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	tRNA-splicing ligase RtcB
Molecular weight formula_weight	54176.1 kDa
EC 编号 ec_number	6.5.1.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C
Atom count atom_count	13603

MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKGAAALEH

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1654

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4dwra1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.261 — Hypothetical protein PH1602
Superfamily Superfamily superfamily	d.261.1 — Hypothetical protein PH1602
Family Family family	d.261.1.1 — Hypothetical protein PH1602

Domain ID domain_id	d4dwra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4dwrb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.261 — Hypothetical protein PH1602
Superfamily Superfamily superfamily	d.261.1 — Hypothetical protein PH1602
Family Family family	d.261.1.1 — Hypothetical protein PH1602

Domain ID domain_id	d4dwrb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4dwrc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.261 — Hypothetical protein PH1602
Superfamily Superfamily superfamily	d.261.1 — Hypothetical protein PH1602
Family Family family	d.261.1.1 — Hypothetical protein PH1602

Domain ID domain_id	d4dwrc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4dwrA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1860 — tRNA-splicing ligase RtcB
Homologous superfamily homologous superfamily	10 — tRNA-splicing ligase RtcB

Domain ID domain_id	4dwrB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1860 — tRNA-splicing ligase RtcB
Homologous superfamily homologous superfamily	10 — tRNA-splicing ligase RtcB

Domain ID domain_id	4dwrC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1860 — tRNA-splicing ligase RtcB
Homologous superfamily homologous superfamily	10 — tRNA-splicing ligase RtcB

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Unit-cell length a length_a	114.081 Å
Unit-cell length b length_b	84.899 Å
Unit-cell length c length_c	124.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	46.740 Å
R factor r_factor	0.1436
R_work r_work	0.1418
R_free r_free	0.1779

RNA ligase RtcB/Mn2+ complex

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

tRNA-splicing ligase RtcB

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

4dwr__assembly_3__model_1

4dwr__assembly_3__model_1 | I(q)

4dwr__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

RNA ligase RtcB/Mn2+ complex

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

tRNA-splicing ligase RtcB

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

4dwr__assembly_3__model_1

4dwr__assembly_3__model_1 | I(q)

4dwr__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)