SAXSdb — 1dd5

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

RIBOSOME RECYCLING FACTOR

Thermotoga maritima

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–185	Not recorded	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；298 K；ammonium sulfate, acetate, glycerol , pH 5.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.55 Å R-free 0.277

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	RRF_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 1–185

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	1dd5
Deposition date deposition_date	1999-11-08
Structure title title	CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF
Keywords keywords	THREE-HELIX BUNDLE, BETA-ALPHA-BETA SANDWICH, RIBOSOME; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.72 Å
Radius of gyration Rg (electron density) rg_electron	22.21 Å
Forward intensity I(0) i0	7726710.00
Molecular weight molecular_weight	21499.0 kDa
Excluded volume excluded_volume	27372 Å³
Envelope volume envelope_volume	33776 Å³
Hydration-shell volume shell_volume	14096 Å³
Envelope diameter envelope_diameter	76.9 Å
Shell Rg shell_rg	26.46 Å
Envelope Rg envelope_rg	22.38 Å
Shape Rg shape_rg	22.23 Å
Total Rg total_rg	22.81 Å
Total atoms total_atoms	1512
Residues n_residues	184
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.9 Å
Rg (real space) rg_real	22.97 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	7.7270e+06
I(0) uncertainty (real space) i0_real_error	1.1670e+05
Rg (reciprocal space) rg_reciprocal	22.91 Å
I(0) (reciprocal space) i0_reciprocal	7726000.0000
Solution quality estimate total_estimate	0.8087
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.517
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2120000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.550; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RIBOSOME RECYCLING FACTOR
Molecular weight formula_weight	21548.0 kDa
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	1577

MVNPFIKEAKEKMKRTLEKIEDELRKMRTGKPSPAILEEIKVDYYGVPTPVNQLATISISEERTLVIKPWDKSVLSLIEKAINASDLGLNPINDGNVIRLVFPSPTTEQREKWVKKAKEIVEEGKIAIRNIRREILKKIKEDQKEGLIPEDDAKRLENEIQKLTDEFIEKLDEVFEIKKEEIMEF

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dd5a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
Superfamily Superfamily superfamily	d.67.3 — Ribosome recycling factor, RRF
Family Family family	d.67.3.1 — Ribosome recycling factor, RRF

CATH v4.4 (2 domains)

Domain ID domain_id	1dd5A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — Ribosome-recycling factor

Domain ID domain_id	1dd5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

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8. Citations (3)

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Unit-cell length a length_a	47.250 Å
Unit-cell length b length_b	47.250 Å
Unit-cell length c length_c	297.550 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2320
R_work r_work	0.2300
R_free r_free	0.2770

fit	/app/data/saxs_computation/dd/1dd5/1dd5.fit
pddf	/app/data/pr_computation/dd/1dd5/1dd5.pr.out
profile	/app/data/saxs_computation/dd/1dd5/1dd5.dat

CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF

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

RIBOSOME RECYCLING FACTOR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution