SAXSdb — 1i2a

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

50S RIBOSOMAL PROTEIN L1P

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 14–232	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

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 1I2A	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 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
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
4LQ4 crystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus Deposited 2013-07-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–211（211 aa）	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

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 1–219； UniProt 14–232

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	1i2a
Deposition date deposition_date	2001-02-07
Structure title title	CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION.
Keywords keywords	RIBOSOMAL PROTEIN, PRIMARY RRNA-BINDING PROTEIN, TRANSLATIONAL REPRESSOR, RIBOSOME; 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	20.48 Å
Radius of gyration Rg (electron density) rg_electron	19.52 Å
Forward intensity I(0) i0	9429810.00
Molecular weight molecular_weight	24035.0 kDa
Excluded volume excluded_volume	30755 Å³
Envelope volume envelope_volume	36688 Å³
Hydration-shell volume shell_volume	16181 Å³
Envelope diameter envelope_diameter	64.2 Å
Shell Rg shell_rg	24.99 Å
Envelope Rg envelope_rg	19.60 Å
Shape Rg shape_rg	19.50 Å
Total Rg total_rg	20.46 Å
Total atoms total_atoms	1688
Residues n_residues	212
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	63.5 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	9.4300e+06
I(0) uncertainty (real space) i0_real_error	1.0460e+05
Rg (reciprocal space) rg_reciprocal	20.44 Å
I(0) (reciprocal space) i0_reciprocal	9430000.0000
Solution quality estimate total_estimate	0.9143
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.645
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1995000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	50S RIBOSOMAL PROTEIN L1P
Molecular weight formula_weight	24842.5 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	1873

MDREALLQAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAVIGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGRYMGVILGPRGKMPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEKGLYHIKDAYVKLTMGPAVKVKKEKAKKK

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	PENTANAL
Molecular weight formula_weight	86.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1i2aa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.24 — Ribosomal protein L1
Superfamily Superfamily superfamily	e.24.1 — Ribosomal protein L1
Family Family family	e.24.1.1 — Ribosomal protein L1

CATH v4.4 (2 domains)

Domain ID domain_id	1i2aA01
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	1i2aA02
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 (2)

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Unit-cell length a length_a	33.577 Å
Unit-cell length b length_b	38.881 Å
Unit-cell length c length_c	54.936 Å
Unit-cell angle α angle_alpha	83.32 °
Unit-cell angle β angle_beta	80.14 °
Unit-cell angle γ angle_gamma	74.72 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2470

fit	/app/data/saxs_computation/i2/1i2a/1i2a.fit
pddf	/app/data/pr_computation/i2/1i2a/1i2a.pr.out
profile	/app/data/saxs_computation/i2/1i2a/1i2a.dat

CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION.

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

50S RIBOSOMAL PROTEIN L1P

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