SAXSdb — 2hvf

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

50S ribosomal protein L9

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–52	Fragment：N-terminal domain Mutation：G34(DAL) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 CL CHLORIDE ION × 4 IMD IMIDAZOLE × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.57 Å R-free 0.208
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–52	Fragment：N-terminal domain Mutation：G34(DAL) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 CL CHLORIDE ION × 8 IMD IMIDAZOLE × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.57 Å R-free 0.208

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 2HVF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CQU SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L9 Deposited 1999-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–56（56 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure AMBIENT	Resolution not provided
1DIV RIBOSOMAL PROTEIN L9 Deposited 1996-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.276
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M	ZN ZINC ION × 3 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M	ZN ZINC ION × 5 CL CHLORIDE ION × 6 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–52（52 aa） Fragment：N-terminal domain Chain B 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M Mutation：K12M	ZN ZINC ION × 16 CL CHLORIDE ION × 20 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–52（52 aa） Fragment：N-terminal domain Chain B 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M Mutation：K12M	ZN ZINC ION × 16 CL CHLORIDE ION × 20 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 1–149（149 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BK 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL9_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–52； UniProt 1–52

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	2hvf
Deposition date deposition_date	2006-07-28
Structure title title	Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA
Keywords keywords	L9, ribosomal protein, NTL9, G34dA, 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	12.33 Å
Radius of gyration Rg (electron density) rg_electron	10.81 Å
Forward intensity I(0) i0	941668.00
Molecular weight molecular_weight	6213.0 kDa
Excluded volume excluded_volume	7703 Å³
Envelope volume envelope_volume	8541 Å³
Hydration-shell volume shell_volume	7190 Å³
Envelope diameter envelope_diameter	38.3 Å
Shell Rg shell_rg	15.70 Å
Envelope Rg envelope_rg	11.21 Å
Shape Rg shape_rg	10.67 Å
Total Rg total_rg	12.48 Å
Total atoms total_atoms	417
Residues n_residues	51
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	39.3 Å
Rg (real space) rg_real	12.27 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	9.4170e+05
I(0) uncertainty (real space) i0_real_error	9.7500e+03
Rg (reciprocal space) rg_reciprocal	12.27 Å
I(0) (reciprocal space) i0_reciprocal	941700.0000
Solution quality estimate total_estimate	0.8175
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.101
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	77810.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 0.997; Sysdev: 1.000; 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 (6)

Entity 1 Entity 1 polymer

Description description	50S ribosomal protein L9
Molecular weight formula_weight	5701.7 kDa
Mutation mutation	G34(DAL)
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	494

MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQALAIEATPANLKALEAQKQ

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2hvfa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.1 — Ribosomal protein L9 N-domain

CATH v4.4 (1 domains)

Domain ID domain_id	2hvfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	10 — Ribosomal protein L9, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	53.517 Å
Unit-cell length b length_b	53.517 Å
Unit-cell length c length_c	36.178 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1620
R_work r_work	0.1590
R_free r_free	0.2080

fit	/app/data/saxs_computation/hv/2hvf/2hvf.fit
pddf	/app/data/pr_computation/hv/2hvf/2hvf.pr.out
profile	/app/data/saxs_computation/hv/2hvf/2hvf.dat

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA

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

50S ribosomal protein L9

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