SAXSdb — 1dd3

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

50S RIBOSOMAL PROTEIN L7/L12

OrganismNot specified

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–128 Chain B； UniProt 1–128 Chain C； UniProt 1–32 Chain D； UniProt 1–32	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；3.6M AMMOMIUM SULFATE 0.1M SODIUM CITRATE 7% (V/V) POLYETHYLENE GLYCOL 200, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.00 Å R-free 0.235

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 1DD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DD4 Crystal structure of ribosomal protein l12 from thermotoga maritim Deposited 1999-11-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–128（128 aa） Chain B 1–128（128 aa） Chain C 1–40（40 aa） Chain D 1–40（40 aa）	Not recorded	TBR HEXATANTALUM DODECABROMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；3.23M AMMONIUM SULFATE, 0.1M CITRATE, 7% (V/V) POLYETHYLENE GLYCOL 200, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.241
1DD4 Crystal structure of ribosomal protein l12 from thermotoga maritim Deposited 1999-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–128（128 aa） Chain B 1–128（128 aa） Chain C 1–40（40 aa） Chain D 1–40（40 aa）	Not recorded	TBR HEXATANTALUM DODECABROMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；3.23M AMMONIUM SULFATE, 0.1M CITRATE, 7% (V/V) POLYETHYLENE GLYCOL 200, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.241
1ZAV Ribosomal Protein L10-L12(NTD) Complex, Space Group P21 Deposited 2005-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain U 1–30（30 aa） Fragment：N-terminal domain Chain V 1–30（30 aa） Fragment：N-terminal domain Chain W 1–30（30 aa） Fragment：N-terminal domain Chain X 1–30（30 aa） Fragment：N-terminal domain Chain Y 1–30（30 aa） Fragment：N-terminal domain Chain Z 1–30（30 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；Na acetate, ethylene glycol, PEG 1000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.274
1ZAW Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form A Deposited 2005-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain U 1–30（30 aa） Fragment：N-terminal domain Chain V 1–30（30 aa） Fragment：N-terminal domain Chain W 1–30（30 aa） Fragment：N-terminal domain Chain X 1–30（30 aa） Fragment：N-terminal domain Chain Y 1–30（30 aa） Fragment：N-terminal domain Chain Z 1–30（30 aa） Fragment：N-terminal domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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, SITTING DROP；pH 7.2；293 K；Hepes, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.272
1ZAX Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form B Deposited 2005-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain U 1–30（30 aa） Fragment：N-terminal domain Chain V 1–30（30 aa） Fragment：N-terminal domain Chain W 1–30（30 aa） Fragment：N-terminal domain Chain X 1–30（30 aa） Fragment：N-terminal domain Chain Y 1–30（30 aa） Fragment：N-terminal domain Chain Z 1–30（30 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；imidazole, MgCl2, MPD, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.286
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BI 1–128（128 aa） Chain BJ 1–128（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL7_THEMA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 1–128 Author chain B； PDBConstruct 1–128； UniProt 1–128 Author chain C； PDBConstruct 1–32； UniProt 1–32 Author chain D； PDBConstruct 1–32； UniProt 1–32

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	1dd3
Deposition date deposition_date	1999-11-08
Structure title title	CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIMA
Keywords keywords	;DIMER FORMATION, FLEXIBILITY, HINGE REGION, FOUR-HELIX-BUNDLE, FIVE-HELIX- BUNDLE, ALPHA-BETA STRUCTURE, HELICAL HAIRPIN, DOMAINS, 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	21.41 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	18114800.00
Molecular weight molecular_weight	34041.0 kDa
Excluded volume excluded_volume	43537 Å³
Envelope volume envelope_volume	49995 Å³
Hydration-shell volume shell_volume	20674 Å³
Envelope diameter envelope_diameter	71.7 Å
Shell Rg shell_rg	26.71 Å
Envelope Rg envelope_rg	20.74 Å
Shape Rg shape_rg	20.57 Å
Total Rg total_rg	21.52 Å
Total atoms total_atoms	2390
Residues n_residues	320
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	69.6 Å
Rg (real space) rg_real	21.38 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.8110e+07
I(0) uncertainty (real space) i0_real_error	2.4240e+05
Rg (reciprocal space) rg_reciprocal	21.38 Å
I(0) (reciprocal space) i0_reciprocal	18110000.0000
Solution quality estimate total_estimate	0.8807
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.336
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4411000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.822

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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 L7/L12
Molecular weight formula_weight	13475.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2637

MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK

Entity 2 Entity 2 polymer

Description description	50S RIBOSOMAL PROTEIN L7/L12
Molecular weight formula_weight	3610.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MTIDEIIEAIEKLTVSELAELVKKLEDKFGVT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dd3a1
Class class	a — All alpha proteins
Fold Fold fold	a.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamily	a.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family family	a.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain

Domain ID domain_id	d1dd3a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.45 — ClpS-like
Superfamily Superfamily superfamily	d.45.1 — ClpS-like
Family Family family	d.45.1.1 — Ribosomal protein L7/12, C-terminal domain

Domain ID domain_id	d1dd3b1
Class class	a — All alpha proteins
Fold Fold fold	a.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamily	a.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family family	a.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain

Domain ID domain_id	d1dd3b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.45 — ClpS-like
Superfamily Superfamily superfamily	d.45.1 — ClpS-like
Family Family family	d.45.1.1 — Ribosomal protein L7/12, C-terminal domain

Domain ID domain_id	d1dd3c_
Class class	a — All alpha proteins
Fold Fold fold	a.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamily	a.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family family	a.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain

Domain ID domain_id	d1dd3d_
Class class	a — All alpha proteins
Fold Fold fold	a.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamily	a.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family family	a.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain

CATH v4.4 (4 domains)

Domain ID domain_id	1dd3A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	710 — Single helix bin

Domain ID domain_id	1dd3A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily	10 — Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS

Domain ID domain_id	1dd3B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	710 — Single helix bin

Domain ID domain_id	1dd3B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily	10 — Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS

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8. Citations (1)

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Unit-cell length a length_a	54.330 Å
Unit-cell length b length_b	89.130 Å
Unit-cell length c length_c	119.630 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2350

fit	/app/data/saxs_computation/dd/1dd3/1dd3.fit
pddf	/app/data/pr_computation/dd/1dd3/1dd3.pr.out
profile	/app/data/saxs_computation/dd/1dd3/1dd3.dat

CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIMA

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

50S RIBOSOMAL PROTEIN L7/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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)