SAXSdb — 1wib

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

60S ribosomal protein L12

Mus musculus

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 2–80	Fragment：N-terminal domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition：0.7mM 13C/15N-PROTEIN 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided

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 1WIB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7LS1 80S ribosome from mouse bound to eEF2 (Class II) Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain k 1–165（165 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.30 Å
7LS2 80S ribosome from mouse bound to eEF2 (Class I) Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain k 1–165（165 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	RL12_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–85； UniProt 2–80

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	1wib
Deposition date deposition_date	2004-05-28
Structure title title	Solution structure of the N-terminal domain from mouse hypothetical protein BAB22488
Keywords keywords	N-terminal domain, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RIBOSOME; RIBOSOME
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.22 Å
Radius of gyration Rg (electron density) rg_electron	16.12 Å
Forward intensity I(0) i0	485871000.00
Molecular weight molecular_weight	185210.0 kDa
Excluded volume excluded_volume	232990 Å³
Envelope volume envelope_volume	68283 Å³
Hydration-shell volume shell_volume	24536 Å³
Envelope diameter envelope_diameter	81.8 Å
Shell Rg shell_rg	30.46 Å
Envelope Rg envelope_rg	24.55 Å
Shape Rg shape_rg	16.12 Å
Total Rg total_rg	16.70 Å
Total atoms total_atoms	26520
Residues n_residues	1840
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	45.6 Å
Rg (real space) rg_real	16.15 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	4.6240e+08
I(0) uncertainty (real space) i0_real_error	4.2510e+06
Rg (reciprocal space) rg_reciprocal	17.36 Å
I(0) (reciprocal space) i0_reciprocal	485900000.0000
Solution quality estimate total_estimate	0.6763
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.8 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	3.7290
Highest regularization parameter α highest_alpha	204200.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.948; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1wiba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamily	d.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family family	d.47.1.1 — Ribosomal L11/L12e N-terminal domain

Domain ID domain_id	d1wiba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1wiba3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1wibA00
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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Description description	60S ribosomal protein L12
Molecular weight formula_weight	9284.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	26520

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

fit	/app/data/saxs_computation/wi/1wib/1wib.fit
pddf	/app/data/pr_computation/wi/1wib/1wib.pr.out
profile	/app/data/saxs_computation/wi/1wib/1wib.dat

Solution structure of the N-terminal domain from mouse hypothetical protein BAB22488

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

60S ribosomal protein L12

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)