SAXSdb — 1mms

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

PROTEIN (RIBOSOMAL PROTEIN L11)

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–140	Not recorded	23S RIBOSOMAL RNA × 1 CD CADMIUM ION × 5 MG MAGNESIUM ION × 10 MMC METHYL MERCURY ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–140	Not recorded	23S RIBOSOMAL RNA × 1 CD CADMIUM ION × 3 MG MAGNESIUM ION × 9 MMC METHYL MERCURY ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254

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 1MMS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain K 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1JQM Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid Deposited 2001-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6	Resolution 18.00 Å
1JQS Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog Deposited 2001-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1JQT Fitting of L11 protein in the low resolution cryo-EM map of E.coli 70S ribosome Deposited 2001-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1MVR Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome Deposited 2002-09-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: octameric	Chain L 1–140（140 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 12.80 Å
1OLN Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA Deposited 2003-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 2–141（140 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 6.2；303 K；Ionic strength (raw mmCIF value) 100 MM NACL, 5 MM MGCL2；Pressure 1	Resolution not provided
1PN7 Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome Deposited 2003-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1PN8 Coordinates of S12, L11 proteins and E-site tRNA from 70S crystal structure separately fitted into the Cryo-EM map of E.coli 70S.EF-G.GDPNP complex. The atomic coordinates originally from the E-site tRNA were fitted in the position of the hybrid P/E-site tRNA. Deposited 2003-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1R2W Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of the 70S ribosome Deposited 2003-09-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 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 9.00 Å
1R2X Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome Deposited 2003-09-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 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 9.00 Å
2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70SEF-GGDP*fusidic acid complex Deposited 2005-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–71（65 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine；pH 7.5；20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine cryo-EM vitrification conditions RAPID-FREEZING IN LIQUID ETHANE	Resolution 11.20 Å
2JQ7 Model for thiostrepton binding to the ribosomal L11-RNA Deposited 2007-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 220；Pressure 1 NMR sample composition 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2K3F Ribosomal protein L11 from Thermotoga maritima Deposited 2008-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 1.2 mM [U-100% 15N] L11, 20 mM potassium phosphate, 50 mM potassium chloride, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain L 8–140（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BL 1–141（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

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.

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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

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

Radius of gyration Rg (Guinier) rg_guinier	28.39 Å
Radius of gyration Rg (electron density) rg_electron	28.80 Å
Forward intensity I(0) i0	135147000.00
Molecular weight molecular_weight	62192.0 kDa
Excluded volume excluded_volume	63993 Å³
Envelope volume envelope_volume	86110 Å³
Hydration-shell volume shell_volume	26064 Å³
Envelope diameter envelope_diameter	101.9 Å
Shell Rg shell_rg	34.27 Å
Envelope Rg envelope_rg	28.76 Å
Shape Rg shape_rg	28.93 Å
Total Rg total_rg	28.90 Å
Total atoms total_atoms	4031
Residues n_residues	319
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	96.5 Å
Rg (real space) rg_real	28.62 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	1.3510e+08
I(0) uncertainty (real space) i0_real_error	2.0740e+06
Rg (reciprocal space) rg_reciprocal	28.55 Å
I(0) (reciprocal space) i0_reciprocal	135100000.0000
Solution quality estimate total_estimate	0.8540
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.536
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5586000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.707; Smooth: 0.964

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

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 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

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7. 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

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8. Citations (4)

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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

fit	/app/data/saxs_computation/mm/1mms/1mms.fit
pddf	/app/data/pr_computation/mm/1mms/1mms.pr.out
profile	/app/data/saxs_computation/mm/1mms/1mms.dat

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

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)