SAXSdb — 1ise

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

Ribosome Recycling Factor

Escherichia coli

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	Mutation：R132G	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；50mM MES-NaOH, PEG 1500, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.297

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.

Other PDB	Difference from Current Entry 1ISE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EK8 CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI Deposited 2000-03-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–185（185 aa）	Not recorded	HG MERCURY (II) ION × 3 DEM DECYLOXY-METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1 M MES-NaOH, 10 % PEG 350 MME, 12 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.30 Å R-free 0.297
1Y69 RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2004-12-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain 8 1–30（30 aa） Fragment：UNP residues 1-30 and 106-185 Chain 8 106–185（80 aa） Fragment：UNP residues 1-30 and 106-185	Mutation：RRF domain II deletion and GGG insertion Mutation：RRF domain II deletion and GGG insertion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.33 Å R-free 0.338
1ZN0 Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF Deposited 2005-05-11	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–185（185 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 15.50 Å
1ZN1 Coordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex Deposited 2005-05-11	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–185（185 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 14.10 Å
2RDO 50S subunit with EF-G(GDPNP) and RRF bound Deposited 2007-09-24	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric	Chain 8 1–185（185 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer PolyMix；pH 7.5；PolyMix cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane by Vitrobot	Resolution 9.10 Å
4V9C Allosteric control of the ribosome by small-molecule antibiotics Deposited 2012-07-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain CY 1–185（185 aa）	Not recorded	MG MAGNESIUM ION × 266 NMY NEOMYCIN × 8 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；291 K；PEG800, MPD, pH 6.5, microbatch, temperature 291K	Resolution 3.30 Å R-free 0.255
4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Deposited 2012-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain AY 2–183（182 aa）	Not recorded	MG MAGNESIUM ION × 271 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K	Resolution 3.00 Å R-free 0.260
4WOI 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2 Deposited 2014-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain AV 1–185（185 aa）	Not recorded	MG MAGNESIUM ION × 269 PAR PAROMOMYCIN × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KCl, KSCN	Resolution 3.00 Å R-free 0.253

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RRF_ECOLI
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	1ise
Deposition date deposition_date	2001-11-30
Structure title title	Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly
Keywords keywords	Translation; TRANSLATION
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	22.95 Å
Radius of gyration Rg (electron density) rg_electron	22.39 Å
Forward intensity I(0) i0	7935530.00
Molecular weight molecular_weight	20390.0 kDa
Excluded volume excluded_volume	25393 Å³
Envelope volume envelope_volume	32792 Å³
Hydration-shell volume shell_volume	13613 Å³
Envelope diameter envelope_diameter	78.5 Å
Shell Rg shell_rg	26.47 Å
Envelope Rg envelope_rg	22.63 Å
Shape Rg shape_rg	22.39 Å
Total Rg total_rg	22.97 Å
Total atoms total_atoms	1428
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	79.1 Å
Rg (real space) rg_real	23.20 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	7.9360e+06
I(0) uncertainty (real space) i0_real_error	1.3410e+05
Rg (reciprocal space) rg_reciprocal	23.14 Å
I(0) (reciprocal space) i0_reciprocal	7935000.0000
Solution quality estimate total_estimate	0.7964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.487
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2074000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.650; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.434; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1isea_
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	1iseA01
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	1iseA02
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 (1)

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Unit-cell length a length_a	46.024 Å
Unit-cell length b length_b	49.267 Å
Unit-cell length c length_c	49.365 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2390
R_free r_free	0.2970

Description description	Ribosome Recycling Factor
Molecular weight formula_weight	20571.5 kDa
Mutation mutation	R132G
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1630

Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly

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

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

fit	/app/data/saxs_computation/is/1ise/1ise.fit
pddf	/app/data/pr_computation/is/1ise/1ise.pr.out
profile	/app/data/saxs_computation/is/1ise/1ise.dat