SAXSdb — 5d8h

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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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 9–221	Fragment：UNP residues 9-221 Mutation：Met changed to SeMet Non-standard monomer：Yes (specific site not provided by mmCIF)	23S ribosomal RNA × 1 50S ribosomal protein L11 × 1 （P54030） THIOSTREPTON × 1 （P0C8P8） 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

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 5D8H	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 mutation/modification 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 mutation/modification 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 mutation/modification 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
5DAR CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII Deposited 2015-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain B 9–221（213 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain E 9–221（213 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

3 other PDB entries and 5 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

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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 1–161	Non-standard monomer：Yes (specific site not provided by mmCIF)	23S ribosomal RNA × 1 50S ribosomal protein L10 × 1 （P54049） THIOSTREPTON × 1 （P0C8P8） 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

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 5D8H	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 mutation/modification 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 mutation/modification 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
5DAR CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII Deposited 2015-08-20	Different mutation/modification 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 mutation/modification 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 4 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

THIOSTREPTON

OrganismNot specified

UniProt P0C8P8

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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain D； UniProt 0–18	Non-standard monomer：Yes (specific site not provided by mmCIF)	23S ribosomal RNA × 1 50S ribosomal protein L10 × 1 （P54049） 50S ribosomal protein L11 × 1 （P54030） 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

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 5D8H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E9W Structure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur Deposited 2000-10-27	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 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；1ML 15.38MG/ML THIOSTREPTON IN CHLOROFORM_ISOAMYL ALCOHOL + 100 MICROL GLYCEROL + 200 MICROL ETHANOL. BATCH METHOD, pH 7.00	Resolution 1.02 Å R-free 0.142
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 B 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
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 C 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
2L2W Thiostrepton Deposited 2010-08-27	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 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton, chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2X Thiostrepton, oxidized at CA-CB bond of residue 9 Deposited 2010-08-27	Different construct Different mutation/modification 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 1–16（16 aa） Fragment：residues 1-16	Mutation：(DCY)9(BB9) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (BB9, 9), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2Y Thiostrepton, epimer form of residue 9 Deposited 2010-08-27	Different construct Different mutation/modification 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 1–16（16 aa） Fragment：residues 1-16	Mutation：(DCY)9C Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (epi,9), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2Z Thiostrepton, reduced at N-CA bond of residue 14 Deposited 2010-08-27	Different construct Different mutation/modification 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 1–17（17 aa）	Mutation：(MH6)14(DSN) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (DSN 14), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 5 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.318
4HP2 Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution Deposited 2012-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–72（17 aa） Fragment：UNP RESIDUES 56-72 Chain B 56–72（17 aa） Fragment：UNP RESIDUES 56-72	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	DMF DIMETHYLFORMAMIDE × 8 ETZ diethyl ether × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；DIMETHYLFORMAMID, DIETHYLETHER, pH 7.00, VAPOR DIFFUSION	Resolution 0.64 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THCL_STRAJ
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–19； UniProt 0–18

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	5d8h
Deposition date deposition_date	2015-08-17
Structure title title	CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
Keywords keywords	ribosome, P-stalk, archaea, ANTIBIOTIC, THIOSTREPTON, 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	26.13 Å
Radius of gyration Rg (electron density) rg_electron	26.24 Å
Forward intensity I(0) i0	111252000.00
Molecular weight molecular_weight	66739.0 kDa
Excluded volume excluded_volume	76400 Å³
Envelope volume envelope_volume	102100 Å³
Hydration-shell volume shell_volume	32159 Å³
Envelope diameter envelope_diameter	86.6 Å
Shell Rg shell_rg	33.73 Å
Envelope Rg envelope_rg	26.08 Å
Shape Rg shape_rg	26.28 Å
Total Rg total_rg	26.79 Å
Total atoms total_atoms	4527
Residues n_residues	434
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	83.5 Å
Rg (real space) rg_real	26.04 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.1130e+08
I(0) uncertainty (real space) i0_real_error	1.4620e+06
Rg (reciprocal space) rg_reciprocal	26.07 Å
I(0) (reciprocal space) i0_reciprocal	111300000.0000
Solution quality estimate total_estimate	0.9028
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.9 Å
Skewness Skewness skewness	0.205
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10340000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	23928.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	4592

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	23635.2 kDa
Mutation mutation	Met changed to SeMet
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

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	17794.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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 polymer

Description description	THIOSTREPTON
Molecular weight formula_weight	1806.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XIASASCTTCICTCSCSSX

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5d8hB01
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	5d8hB02
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	5d8hC01
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	125.070 Å
Unit-cell length b length_b	127.160 Å
Unit-cell length c length_c	132.930 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	45.545 Å
R factor r_factor	0.2099
R_work r_work	0.2081
R_free r_free	0.2450

fit	/app/data/saxs_computation/d8/5d8h/5d8h.fit
pddf	/app/data/pr_computation/d8/5d8h/5d8h.pr.out
profile	/app/data/saxs_computation/d8/5d8h/5d8h.dat

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

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

THIOSTREPTON

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 (8)

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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)