SAXSdb — 1zav

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

50S ribosomal protein L10

Thermotoga maritima

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–179	Not recorded	50S ribosomal protein L7/L12 × 6 （P29396）	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

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 1ZAV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZAW Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form A Deposited 2005-04-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–179（179 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, 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–179（179 aa）	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

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

View Construct and Data Evidence

UniProt name	RL10_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–180； UniProt 1–179

50S ribosomal protein L7/L12

Thermotoga maritima

UniProt P29396

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain U； UniProt 1–30 Chain V； UniProt 1–30 Chain W； UniProt 1–30 Chain X； UniProt 1–30 Chain Y； UniProt 1–30 Chain Z； UniProt 1–30	Fragment：N-terminal domain	50S ribosomal protein L10 × 1 （P29394）	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

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 1ZAV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DD3 CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIMA Deposited 1999-11-08	Different construct Different mutation/modification Different oligomeric state 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 1–32（32 aa） Chain D 1–32（32 aa）	Not recorded	No recorded non-water small molecule	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
1DD4 Crystal structure of ribosomal protein l12 from thermotoga maritim Deposited 1999-11-08	Different construct Different mutation/modification Different oligomeric state 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 mutation/modification 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
1ZAW Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form A Deposited 2005-04-07	Different mutation/modification 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 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	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–30； UniProt 1–30 Author chain V； PDBConstruct 1–30； UniProt 1–30 Author chain W； PDBConstruct 1–30； UniProt 1–30 Author chain X； PDBConstruct 1–30； UniProt 1–30 Author chain Y； PDBConstruct 1–30； UniProt 1–30 Author chain Z； PDBConstruct 1–30； UniProt 1–30

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	1zav
Deposition date deposition_date	2005-04-07
Structure title title	Ribosomal Protein L10-L12(NTD) Complex, Space Group P21
Keywords keywords	;ribosome structure and function, L10-L12 complex structure, L10E structure, L7/12 ribosomal stalk, thiostrepton loop of 23S rRNA, translation factor recruitment, GTPase stimulation, mechanism of translation, rapid kinetics, STRUCTURAL PROTEIN ;; STRUCTURAL 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	30.16 Å
Radius of gyration Rg (electron density) rg_electron	29.98 Å
Forward intensity I(0) i0	22424900.00
Molecular weight molecular_weight	40091.0 kDa
Excluded volume excluded_volume	51765 Å³
Envelope volume envelope_volume	67516 Å³
Hydration-shell volume shell_volume	20600 Å³
Envelope diameter envelope_diameter	108.4 Å
Shell Rg shell_rg	33.99 Å
Envelope Rg envelope_rg	29.79 Å
Shape Rg shape_rg	29.92 Å
Total Rg total_rg	30.65 Å
Total atoms total_atoms	2818
Residues n_residues	353
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	104.0 Å
Rg (real space) rg_real	30.49 Å
Rg uncertainty (real space) rg_real_error	1.32 Å
I(0) (real space) i0_real	2.2420e+07
I(0) uncertainty (real space) i0_real_error	3.7980e+05
Rg (reciprocal space) rg_reciprocal	30.35 Å
I(0) (reciprocal space) i0_reciprocal	22420000.0000
Solution quality estimate total_estimate	0.7708
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.469
Kurtosis Kurtosis kurtosis	-0.557
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10850000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.561; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.413; Smooth: 0.928

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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 L10
Molecular weight formula_weight	20436.9 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	3247

VMLTRQQKELIVKEMSEIFKKTSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEEFLKGPTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGKKFTAEEVENIAKLPSKEELYAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEKKSE

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L7/L12
Molecular weight formula_weight	3410.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V,W,X,Y,Z

MTIDEIIEAIEKLTVSELAELVKKLEDKFG

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	413

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1zava1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.62 — Ribosomal protein L10-like
Family Family family	d.58.62.1 — Ribosomal protein L10-like

Domain ID domain_id	d1zava2
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	d1zavu1
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	d1zavv1
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	d1zavw1
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	d1zavx1
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	d1zavy1
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	d1zavz1
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 (2 domains)

Domain ID domain_id	1zavA01
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	1zavA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	290 —

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8. Citations (1)

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Unit-cell length a length_a	43.438 Å
Unit-cell length b length_b	60.375 Å
Unit-cell length c length_c	83.372 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2390
R_work r_work	0.2260
R_free r_free	0.2740

fit	/app/data/saxs_computation/za/1zav/1zav.fit
pddf	/app/data/pr_computation/za/1zav/1zav.pr.out
profile	/app/data/saxs_computation/za/1zav/1zav.dat

Ribosomal Protein L10-L12(NTD) Complex, Space Group P21

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 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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (8 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)