SAXSdb — 5dar

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

50S ribosomal protein L10

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 9–221	Not recorded	74 nt fragment of 23S rRNA × 1 50S ribosomal protein L11 × 1 （P54030） 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
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain E； UniProt 9–221	Not recorded	74 nt fragment of 23S rRNA × 1 50S ribosomal protein L11 × 1 （P54030） 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

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 5DAR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JSY N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii Deposited 2009-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–221（212 aa） Fragment：N-terminal fragment, residues in UNP 10-221	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；KSCN, PEG4000, NaAcetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233
3JSY N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii Deposited 2009-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 10–221（212 aa） Fragment：N-terminal fragment, residues in UNP 10-221	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；KSCN, PEG4000, NaAcetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233
5D6G CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII Deposited 2015-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 10–221（212 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；50 mM Sodium Cacodylate, pH 6.5, 0.2 M KCl, 0.1 M Magnesium acetate, 9% PEG 6000, 0.5 mM CTAB	Resolution 3.30 Å R-free 0.298
5D8H CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON Deposited 2015-08-17	Different construct 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 B 9–221（213 aa） Fragment：UNP residues 9-221	Mutation：Met changed to SeMet 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

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL10_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–213； UniProt 9–221 Author chain E； PDBConstruct 1–213； UniProt 9–221

50S ribosomal protein L11

Methanocaldococcus jannaschii

UniProt P54030

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 Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 1–161	Not recorded	74 nt fragment of 23S rRNA × 1 50S ribosomal protein L10 × 1 （P54049） 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
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain F； UniProt 1–161	Not recorded	74 nt fragment of 23S rRNA × 1 50S ribosomal protein L10 × 1 （P54049） 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

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 5DAR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5COL RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII Deposited 2015-07-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–161（161 aa）	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
5COL RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII Deposited 2015-07-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–161（161 aa）	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
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

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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–161； UniProt 1–161 Author chain F； 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	5dar
Deposition date deposition_date	2015-08-20
Structure title title	CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII
Keywords keywords	ribosome, P-stalk, archaea, ribosomal protein; RIBOSOMAL PROTEIN
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	35.43 Å
Radius of gyration Rg (electron density) rg_electron	35.53 Å
Forward intensity I(0) i0	362092000.00
Molecular weight molecular_weight	122910.0 kDa
Excluded volume excluded_volume	140640 Å³
Envelope volume envelope_volume	199440 Å³
Hydration-shell volume shell_volume	47126 Å³
Envelope diameter envelope_diameter	124.5 Å
Shell Rg shell_rg	41.50 Å
Envelope Rg envelope_rg	35.27 Å
Shape Rg shape_rg	35.54 Å
Total Rg total_rg	35.82 Å
Total atoms total_atoms	8400
Residues n_residues	829
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	114.9 Å
Rg (real space) rg_real	35.51 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	3.6210e+08
I(0) uncertainty (real space) i0_real_error	7.1290e+06
Rg (reciprocal space) rg_reciprocal	35.46 Å
I(0) (reciprocal space) i0_reciprocal	362100000.0000
Solution quality estimate total_estimate	0.6878
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.9 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13950000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.987; Smooth: 0.644

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	74 nt fragment of 23S rRNA
Molecular weight formula_weight	23928.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A,D
Atom count atom_count	8414

GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGCUCACCCGUCGAGGC

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 polymer

Description description	50S ribosomal protein L10
Molecular weight formula_weight	23353.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI

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 3 Entity 3 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	C,F

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 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	8

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5darC01
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	5darE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1730 — Ribosomal protein L10, N-terminal RNA-binding domain

Domain ID domain_id	5darE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
Homologous superfamily homologous superfamily	20 — Ribosomal protein L10, N-terminal fragment, domain II

Domain ID domain_id	5darF01
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	72.396 Å
Unit-cell length b length_b	88.451 Å
Unit-cell length c length_c	95.231 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2661
R_work r_work	0.2644
R_free r_free	0.2968

fit	/app/data/saxs_computation/da/5dar/5dar.fit
pddf	/app/data/pr_computation/da/5dar/5dar.pr.out
profile	/app/data/saxs_computation/da/5dar/5dar.dat

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII

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

50S ribosomal protein L10

State in the Current Structure

Other States of the Same Protein in the Database

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)