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9rk9

Fervidolysin B (FerB) from Fervidobacterium pennivorans

Method: X-RAY DIFFRACTION D_max: 71.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rk9
deposition_date	2025-06-13
last_revision	2026-06-10
title	Fervidolysin B (FerB) from Fervidobacterium pennivorans
keywords	Protease, keratinase, Subtilisin-like S8 endopeptidase, FerB, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.72 Å
rg_electron	20.84 Å
i0	34412400.00
molecular_weight	45489.0 kDa
excluded_volume	56903 Å³
envelope_volume	62935 Å³
shell_volume	24754 Å³
envelope_diameter	73.1 Å
shell_rg	28.24 Å
envelope_rg	21.31 Å
shape_rg	20.84 Å
total_rg	21.72 Å
total_atoms	3208
n_residues	408
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

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3. P(r) Analysis (GNOM)

dmax	71.1 Å
rg_real	21.66 Å
rg_real_error	0.37 Å
i0_real	3.4410e+07
i0_real_error	4.1120e+05
rg_reciprocal	21.67 Å
i0_reciprocal	34410000.0000
total_estimate	0.8787
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.333
kurtosis	-0.197
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	11200000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Subtilisin-like serine protease
formula_weight	10853.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3558

MNSLEPRFEPRAQGEFEVSEKLGVSGTEEDYVPGEYVVQFEPREDAVKALSSVGAEVVRAYSFSDVQIVTVRTEKPELLNSLPGVKSVDKNYIYRAL

Source

organism	Fervidobacterium pennivorans
ncbi_taxonomy_id	93466
host_organism	Escherichia coli

Entity 2 polymer

description	Subtilisin-like serine protease
formula_weight	36354.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ATPNDTYYRYQWHYNNIKLPQAWDIMKSANIVVAVIDTGVSFTHPDLQGIFVQGYDFVDGDYDPTDPAQDVSHGTHCIGTIAAVTNNSLGVAGVNWGGYGIKIMPIRVLGADGSGTLDNVAAGIRWAVDNGAKIVSMSLGGSGAQVLMDAVKYAYSRNVTLICAAGNESRPSLSYPAAYVETIAVGATRYDNTRARYSNYNYTRYYDPYRKAYVYHYLDVVAPGGDTSVDQNGDGYADGVLSTTWTPTYGNTYMFLQGTSMATPHVAALAAMLYAKGYTTPEAIRSRLIKTAYKIPGYTYNSSGWNKYVGYGLIDAYKALTYSAHHHHHHHH

Source

organism	Fervidobacterium pennivorans
ncbi_taxonomy_id	93466
host_organism	Escherichia coli

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	nat
entity_count	2

Entity 7 non-polymer

description	CITRIC ACID
formula_weight	192.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	327

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6. Citations (1)

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length_a	53.574 Å
length_b	71.829 Å
length_c	141.070 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.490 Å
resolution_low	64.010 Å
r_factor	0.1741
r_work	0.1736
r_free	0.1949

fit	/app/data/saxs_computation/rk/9rk9/9rk9.fit
pddf	/app/data/pr_computation/rk/9rk9/9rk9.pr.out
profile	/app/data/saxs_computation/rk/9rk9/9rk9.dat

Fervidolysin B (FerB) from Fervidobacterium pennivorans

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)