SAXSdb — 1d6t

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

RIBONUCLEASE P

Staphylococcus aureus

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 1–117	Not recorded	No other associated polymer	SOLUTION NMR NMR sample composition：1.5mM RNAseP protein, U-15N,13C, pH 6.0, (500mM sodium chloride, 20mM sodium acetate, 20mM sodium phosphate) \| 95% H2O/5% 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 1D6T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6D1R Structure of Staphylococcus aureus RNase P protein at 2.0 angstrom Deposited 2018-04-12	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–117（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298.15 K；3.3M (NH4)2SO4, 0.15M potassium phosphate pH6.5	Resolution 2.00 Å R-free 0.234
6OV1 Structure of Staphylococcus aureus RNase P protein mutant with defective mRNA degradation activity Deposited 2019-05-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–117（114 aa）	Mutation：P89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298.15 K；0.1 M Imidazole-HCl, pH8 1.3 M Sodium Citrate	Resolution 1.66 Å R-free 0.238
6OV1 Structure of Staphylococcus aureus RNase P protein mutant with defective mRNA degradation activity Deposited 2019-05-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–117（114 aa）	Mutation：P89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298.15 K；0.1 M Imidazole-HCl, pH8 1.3 M Sodium Citrate	Resolution 1.66 Å R-free 0.238

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNPA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 1–117

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	1d6t
Deposition date deposition_date	1999-10-15
Structure title title	RNASE P PROTEIN FROM STAPHYLOCOCCUS AUREUS
Keywords keywords	ENDONUCLEASE, RNASE, SUBUNIT, HYDROLASE; HYDROLASE
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	14.03 Å
Radius of gyration Rg (electron density) rg_electron	13.85 Å
Forward intensity I(0) i0	824370000.00
Molecular weight molecular_weight	266940.0 kDa
Excluded volume excluded_volume	344640 Å³
Envelope volume envelope_volume	34497 Å³
Hydration-shell volume shell_volume	17218 Å³
Envelope diameter envelope_diameter	53.8 Å
Shell Rg shell_rg	22.99 Å
Envelope Rg envelope_rg	16.84 Å
Shape Rg shape_rg	13.77 Å
Total Rg total_rg	14.34 Å
Total atoms total_atoms	18840
Residues n_residues	2340
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	45.7 Å
Rg (real space) rg_real	13.94 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	8.2440e+08
I(0) uncertainty (real space) i0_real_error	8.0780e+06
Rg (reciprocal space) rg_reciprocal	13.95 Å
I(0) (reciprocal space) i0_reciprocal	824400000.0000
Solution quality estimate total_estimate	0.8079
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	305500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 0.998; 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 (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d6ta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.2 — RNase P protein

CATH v4.4 (1 domains)

Domain ID domain_id	1d6tA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	RIBONUCLEASE P
Molecular weight formula_weight	13684.3 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	18840

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21

RNASE P PROTEIN FROM STAPHYLOCOCCUS AUREUS

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

RIBONUCLEASE P

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/d6/1d6t/1d6t.fit
pddf	/app/data/pr_computation/d6/1d6t/1d6t.pr.out
profile	/app/data/saxs_computation/d6/1d6t/1d6t.dat