SAXSdb — 4lq4

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

50S ribosomal protein L1

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 1–211	Not recorded	TLA L(+)-TARTARIC ACID × 1 IPA ISOPROPYL ALCOHOL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% PEG4000, 10% isopropanol, 0.1 M Hepes-NaOH, 0.5 mkl 0.8 KNa-tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.220

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 4LQ4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJS CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS JANNASCHII Deposited 1999-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–232（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；pH 7.50, VAPOR DIFFUSION	Resolution 2.30 Å R-free 0.271
1I2A CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION. Deposited 2001-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–232（219 aa）	Not recorded	PTL PENTANAL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；301.5 K；PEG 10000, HEPES-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301.5K	Resolution 1.85 Å R-free 0.247
1U63 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-mRNA COMPLEX Deposited 2004-07-29	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 1–219（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；PEG 10000, MPD, KCL, NACl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.40 Å R-free 0.302
1U63 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-mRNA COMPLEX Deposited 2004-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–219（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；PEG 10000, MPD, KCL, NACl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.40 Å R-free 0.302

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

View Construct and Data Evidence

UniProt name	RL1_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1–211

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	4lq4
Deposition date deposition_date	2013-07-17
Structure title title	crystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus
Keywords keywords	;Beta-Alpha-Beta, structural constituent of ribosome, rRNA binding, regulation of translation, translation, Ribosomal RNA, mRNA, 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	20.54 Å
Radius of gyration Rg (electron density) rg_electron	19.47 Å
Forward intensity I(0) i0	9759600.00
Molecular weight molecular_weight	24153.0 kDa
Excluded volume excluded_volume	30766 Å³
Envelope volume envelope_volume	36707 Å³
Hydration-shell volume shell_volume	16210 Å³
Envelope diameter envelope_diameter	64.9 Å
Shell Rg shell_rg	25.09 Å
Envelope Rg envelope_rg	19.60 Å
Shape Rg shape_rg	19.46 Å
Total Rg total_rg	20.39 Å
Total atoms total_atoms	1691
Residues n_residues	211
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	76.3 Å
Rg (real space) rg_real	20.49 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	9.7600e+06
I(0) uncertainty (real space) i0_real_error	1.4300e+05
Rg (reciprocal space) rg_reciprocal	20.50 Å
I(0) (reciprocal space) i0_reciprocal	9760000.0000
Solution quality estimate total_estimate	0.7637
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.635
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2565000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.826; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	50S ribosomal protein L1
Molecular weight formula_weight	23867.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1914

MDREALLQAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAVIGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGRYMGVILGPRGKMPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEKGLYHIKDAYVKLTMGPAVKV

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	243232
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4lq4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	4lq4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

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8. Citations (1)

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Unit-cell length a length_a	33.868 Å
Unit-cell length b length_b	105.255 Å
Unit-cell length c length_c	38.526 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	32.860 Å
R factor r_factor	0.1673
R_work r_work	0.1644
R_free r_free	0.2203

fit	/app/data/saxs_computation/lq/4lq4/4lq4.fit
pddf	/app/data/pr_computation/lq/4lq4/4lq4.pr.out
profile	/app/data/saxs_computation/lq/4lq4/4lq4.dat

crystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus

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

50S ribosomal protein L1

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