SAXSdb — 1mms

▼

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

PROTEIN (RIBOSOMAL PROTEIN L11)

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	23S RIBOSOMAL RNA × 1 CADMIUM ION × 5 MAGNESIUM ION × 10 METHYL MERCURY ION × 5 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	23S RIBOSOMAL RNA × 1 CADMIUM ION × 3 MAGNESIUM ION × 9 METHYL MERCURY ION × 3 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL11_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 1–140 Author chain B； PDBConstruct 1–140； UniProt 1–140

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1mms
Deposition date deposition_date	1999-04-14
Structure title title	Crystal structure of the ribosomal PROTEIN L11-RNA complex
Keywords keywords	RNA-PROTEIN COMPLEX, RNA, RIBOSOME, TRANSLOCATION, THIOSTREPTON; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1mms__assembly_1__model_1

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

Download this curve (.dat)

1mms__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mms__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.33 Å
Rg (electron density)	19.16 Å
Total Rg	19.70 Å
Atom count	2256
Residues	191
Excluded volume	36441 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mms__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mms__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	23S RIBOSOMAL RNA
Molecular weight formula_weight	18693.1 kDa
Mutation mutation	U1108C
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4173

GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC

Entity 2 Entity 2 polymer

Description description	PROTEIN (RIBOSOMAL PROTEIN L11)
Molecular weight formula_weight	14980.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 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	19

Entity 5 Entity 5 non-polymer

Description description	METHYL MERCURY ION
Molecular weight formula_weight	215.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1mmsa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.7 — Ribosomal protein L11, C-terminal domain
Family Family family	a.4.7.1 — Ribosomal protein L11, C-terminal domain

Domain ID domain_id	d1mmsa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamily	d.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family family	d.47.1.1 — Ribosomal L11/L12e N-terminal domain

Domain ID domain_id	d1mmsb_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.7 — Ribosomal protein L11, C-terminal domain
Family Family family	a.4.7.1 — Ribosomal protein L11, C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1mmsA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1550 — Ribosomal protein L11, N-terminal domain
Homologous superfamily homologous superfamily	10 — Ribosomal protein L11/L12, N-terminal domain

Domain ID domain_id	1mmsA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	250 — Ribosomal protein L11/L12, C-terminal domain

Domain ID domain_id	1mmsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	250 — Ribosomal protein L11/L12, C-terminal domain

▶

Unit-cell length a length_a	63.890 Å
Unit-cell length b length_b	84.260 Å
Unit-cell length c length_c	155.510 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2190
R_free r_free	0.2540

Crystal structure of the ribosomal PROTEIN L11-RNA complex

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

PROTEIN (RIBOSOMAL PROTEIN L11)

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

1mms__assembly_1__model_1

1mms__assembly_1__model_1 | I(q)

1mms__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

Source Source

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)

Crystal structure of the ribosomal PROTEIN L11-RNA complex

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

PROTEIN (RIBOSOMAL PROTEIN L11)

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

1mms__assembly_1__model_1

1mms__assembly_1__model_1 | I(q)

1mms__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

Source Source

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)