SAXSdb — 1a6f

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

RIBONUCLEASE P PROTEIN

Bacillus subtilis

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 2–116	Mutation：ALA 2, HIS 3, LEU 4 ARE INSERTED BETWEEN MET 1 AND LYS 2	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.317
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–116	Mutation：ALA 2, HIS 3, LEU 4 ARE INSERTED BETWEEN MET 1 AND LYS 2	ZN ZINC ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.317

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	RNPA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–119； UniProt 2–116

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	1a6f
Deposition date deposition_date	1998-02-24
Structure title title	RNASE P PROTEIN FROM BACILLUS SUBTILIS
Keywords keywords	ENDONUCLEASE, RNASE, SUBUNIT; ENDONUCLEASE
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	15.16 Å
Radius of gyration Rg (electron density) rg_electron	13.53 Å
Forward intensity I(0) i0	3819400.00
Molecular weight molecular_weight	13698.0 kDa
Excluded volume excluded_volume	17204 Å³
Envelope volume envelope_volume	19243 Å³
Hydration-shell volume shell_volume	12005 Å³
Envelope diameter envelope_diameter	43.8 Å
Shell Rg shell_rg	19.44 Å
Envelope Rg envelope_rg	13.85 Å
Shape Rg shape_rg	13.43 Å
Total Rg total_rg	15.07 Å
Total atoms total_atoms	957
Residues n_residues	113
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	46.3 Å
Rg (real space) rg_real	15.03 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.8190e+06
I(0) uncertainty (real space) i0_real_error	4.3660e+04
Rg (reciprocal space) rg_reciprocal	15.04 Å
I(0) (reciprocal space) i0_reciprocal	3819000.0000
Solution quality estimate total_estimate	0.8990
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.065
Kurtosis Kurtosis kurtosis	-0.424
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	805800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RIBONUCLEASE P PROTEIN
Molecular weight formula_weight	14154.5 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	ALA 2, HIS 3, LEU 4 ARE INSERTED BETWEEN MET 1 AND LYS 2
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	967

MAHLKKRNRLKKNEDFQKVFKHGTSVANRQFVLYTLDQPENDELRVGLSVSKKIGNAVMRNRIKRLIRQAFLEEKERLKEKDYIIIARKPASQLTYEETKKSLQHLFRKSSLYKKSSSK

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a6fa_
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	1a6fA00
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	82.400 Å
Unit-cell length b length_b	82.400 Å
Unit-cell length c length_c	33.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.3170

fit	/app/data/saxs_computation/a6/1a6f/1a6f.fit
pddf	/app/data/pr_computation/a6/1a6f/1a6f.pr.out
profile	/app/data/saxs_computation/a6/1a6f/1a6f.dat

RNASE P PROTEIN FROM BACILLUS SUBTILIS

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

RIBONUCLEASE P PROTEIN

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