SAXSdb — 5col

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

50S ribosomal protein L11

Methanocaldococcus jannaschii

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 1–161	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM Sodium Citrate, pH 5.0, 0.1 M MgCl2, 27% PEG 600	Resolution 2.25 Å R-free 0.252
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–161	Not recorded	PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM Sodium Citrate, pH 5.0, 0.1 M MgCl2, 27% PEG 600	Resolution 2.25 Å R-free 0.252

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 5COL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5D8H CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON Deposited 2015-08-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–161（161 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 11 NA SODIUM ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 mM Tris-HCl, pH 7.5, 10% PEG 8000, 20% glycerol, 1 mM TCEP (tris(2-carboxyethyl)phosphine), 0.125 mM CTAB	Resolution 2.80 Å R-free 0.245
5DAR CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII Deposited 2015-08-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain C 1–161（161 aa）	Not recorded	MG MAGNESIUM ION × 5 CL CHLORIDE ION × 2 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris-HCl, pH 7.5, 0.15 M KCl, 20 mM MgCl2, 15% PEG 4000	Resolution 2.90 Å R-free 0.297
5DAR CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII Deposited 2015-08-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain F 1–161（161 aa）	Not recorded	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris-HCl, pH 7.5, 0.15 M KCl, 20 mM MgCl2, 15% PEG 4000	Resolution 2.90 Å R-free 0.297

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL11_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 1–161 Author chain B； PDBConstruct 1–161； UniProt 1–161

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	5col
Deposition date deposition_date	2015-07-20
Structure title title	RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII
Keywords keywords	Archaeal Proteins, Methanococcus, Protein Structure, RNA, Ribosomal Proteins, Ribosomes, 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	21.81 Å
Radius of gyration Rg (electron density) rg_electron	20.67 Å
Forward intensity I(0) i0	18401000.00
Molecular weight molecular_weight	33607.0 kDa
Excluded volume excluded_volume	42744 Å³
Envelope volume envelope_volume	51870 Å³
Hydration-shell volume shell_volume	21363 Å³
Envelope diameter envelope_diameter	69.7 Å
Shell Rg shell_rg	26.74 Å
Envelope Rg envelope_rg	20.66 Å
Shape Rg shape_rg	20.70 Å
Total Rg total_rg	21.44 Å
Total atoms total_atoms	2351
Residues n_residues	307
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	67.6 Å
Rg (real space) rg_real	21.69 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.8400e+07
I(0) uncertainty (real space) i0_real_error	2.4640e+05
Rg (reciprocal space) rg_reciprocal	21.71 Å
I(0) (reciprocal space) i0_reciprocal	18400000.0000
Solution quality estimate total_estimate	0.7258
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.144
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4803000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 1.000; Smooth: 0.984

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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	50S ribosomal protein L11
Molecular weight formula_weight	17513.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2385

MAKEVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVDTETRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSYTLKNAVKEVLGTCGSMGVTVEGKDPKEVQKEIDAGVYDEYFKEE

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5colA01
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	5colB01
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

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8. Citations (1)

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Unit-cell length a length_a	69.150 Å
Unit-cell length b length_b	88.050 Å
Unit-cell length c length_c	142.920 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	44.030 Å
R factor r_factor	0.2170
R_work r_work	0.2151
R_free r_free	0.2524

fit	/app/data/saxs_computation/co/5col/5col.fit
pddf	/app/data/pr_computation/co/5col/5col.pr.out
profile	/app/data/saxs_computation/co/5col/5col.dat

RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII

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

50S 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