← Back to search

9y1l

Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y1l
deposition_date	2025-08-29
last_revision	2025-09-10
title	Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK
keywords	Restriction endonuclease, Structural Genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.87 Å
rg_electron	19.55 Å
i0	19774000.00
molecular_weight	33940.0 kDa
excluded_volume	42595 Å³
envelope_volume	50655 Å³
shell_volume	21434 Å³
envelope_diameter	68.8 Å
shell_rg	26.09 Å
envelope_rg	19.73 Å
shape_rg	19.54 Å
total_rg	20.49 Å
total_atoms	2400
n_residues	304
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	66.7 Å
rg_real	20.76 Å
rg_real_error	0.35 Å
i0_real	1.9770e+07
i0_real_error	2.7160e+05
rg_reciprocal	20.78 Å
i0_reciprocal	19770000.0000
total_estimate	0.8906
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.1 Å
skewness	0.218
kurtosis	-0.364
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	4723000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.983

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Putative restriction endonuclease domain-containing protein
formula_weight	21087.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2656

MTTVRPKEWTYEEFMALPEGGPLHYEIIDGELTMTPAPNTRHQEISGNLFRIISTFLHGNPGSGKVFSAPTDVILSHDPLRAVEPDLVFVSKDRLSLIGEKNIEGAPDLLVEILSEGTEKRDRREKFALYERSGVPEYWIVDPDTNTVQVFRLSGNTYQSPAEFRRQDVLASPLLPGLSIPLSEVFPS

Source

organism	Leptospirillum ferriphilum YSK
ncbi_taxonomy_id	1441628
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	185

▶

6. Citations (1)

▶

length_a	76.989 Å
length_b	76.989 Å
length_c	45.840 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31
int_tables_number	144
crystal_system	—

resolution	1.650 Å
resolution_low	26.961 Å
r_factor	—
r_work	0.1544
r_free	0.1775

fit	/app/data/saxs_computation/y1/9y1l/9y1l.fit
pddf	/app/data/pr_computation/y1/9y1l/9y1l.pr.out
profile	/app/data/saxs_computation/y1/9y1l/9y1l.dat