SAXSdb — 6ov1

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

Ribonuclease P protein component

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 4–117	Mutation：P89A	No other associated polymer	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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 4–117	Mutation：P89A	No other associated polymer	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

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 6OV1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D6T RNASE P PROTEIN FROM STAPHYLOCOCCUS AUREUS Deposited 1999-10-15	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	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
6D1R Structure of Staphylococcus aureus RNase P protein at 2.0 angstrom Deposited 2018-04-12	Different mutation/modification 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

2 other PDB entries and 2 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 24–137； UniProt 4–117 Author chain B； PDBConstruct 24–137； UniProt 4–117

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	6ov1
Deposition date deposition_date	2019-05-06
Structure title title	Structure of Staphylococcus aureus RNase P protein mutant with defective mRNA degradation activity
Keywords keywords	RNase P protein, tRNA processing, mRNA degradation, RNA binding protein; RNA BINDING 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	21.40 Å
Radius of gyration Rg (electron density) rg_electron	20.70 Å
Forward intensity I(0) i0	12548400.00
Molecular weight molecular_weight	26900.0 kDa
Excluded volume excluded_volume	33948 Å³
Envelope volume envelope_volume	42434 Å³
Hydration-shell volume shell_volume	17894 Å³
Envelope diameter envelope_diameter	84.2 Å
Shell Rg shell_rg	26.36 Å
Envelope Rg envelope_rg	21.31 Å
Shape Rg shape_rg	20.71 Å
Total Rg total_rg	21.53 Å
Total atoms total_atoms	3783
Residues n_residues	241
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	80.4 Å
Rg (real space) rg_real	21.51 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.2550e+07
I(0) uncertainty (real space) i0_real_error	1.6310e+05
Rg (reciprocal space) rg_reciprocal	21.49 Å
I(0) (reciprocal space) i0_reciprocal	12550000.0000
Solution quality estimate total_estimate	0.7295
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.549
Kurtosis Kurtosis kurtosis	0.189
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1652000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.557; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.808; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ov1a1
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

Domain ID domain_id	d6ov1a2
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	d6ov1b1
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

Domain ID domain_id	d6ov1b2
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

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8. Citations (1)

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Unit-cell length a length_a	40.386 Å
Unit-cell length b length_b	43.467 Å
Unit-cell length c length_c	45.837 Å
Unit-cell angle α angle_alpha	91.11 °
Unit-cell angle β angle_beta	114.83 °
Unit-cell angle γ angle_gamma	110.95 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.660 Å
Low-resolution limit resolution_low	40.761 Å
R factor r_factor	0.1905
R_work r_work	0.1869
R_free r_free	0.2384

Description description	Ribonuclease P protein component
Molecular weight formula_weight	15906.6 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	P89A
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3909

Structure of Staphylococcus aureus RNase P protein mutant with defective mRNA degradation activity

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

Ribonuclease P protein component

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

fit	/app/data/saxs_computation/ov/6ov1/6ov1.fit
pddf	/app/data/pr_computation/ov/6ov1/6ov1.pr.out
profile	/app/data/saxs_computation/ov/6ov1/6ov1.dat