SAXSdb — 1bkc

▼

1. Structure Basics

entry_id	1bkc
deposition_date	1998-04-23
title	CATALYTIC DOMAIN OF TNF-ALPHA CONVERTING ENZYME (TACE)
keywords	ZN-ENDOPEPTIDASE, HYDROLASE, TNF-ALPHA; ZN-ENDOPEPTIDASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	38.99 Å
rg_electron	38.85 Å
i0	219352000.00
molecular_weight	116900.0 kDa
excluded_volume	144900 Å³
envelope_volume	200090 Å³
shell_volume	44691 Å³
envelope_diameter	139.1 Å
shell_rg	42.70 Å
envelope_rg	37.96 Å
shape_rg	38.84 Å
total_rg	39.10 Å
total_atoms	8202
n_residues	1019
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	135.0 Å
rg_real	39.15 Å
rg_real_error	1.24 Å
i0_real	2.1940e+08
i0_real_error	3.8020e+06
rg_reciprocal	39.06 Å
i0_reciprocal	219300000.0000
total_estimate	0.8511
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.7 Å
skewness	0.398
kurtosis	-0.195
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	22130000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.783

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
formula_weight	28954.5 kDa
mutation	S266A, N452Q
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	9822

DPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTAWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHELGHNFGAEHDPDGLAECAPNEDQGGKYVMYPIAVSGDHENNKMFSQCSKQSIYKTIESKAQECFQERS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 2 polymer

description	TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
formula_weight	28970.5 kDa
mutation	S266A, N452Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

DPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTAWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHELGHNFGAEHDPDGKAECAPNEDQGGKYVMYPIAVSGDHENNKMFSQCSKQSIYKTIESKAQECFQERS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 3 polymer

description	TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
formula_weight	28968.5 kDa
mutation	S266A, N452Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTAWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHELGHNFGAEHDPDGLAECAPNEEQGGKYVMYPIAVSGDHENNKMFSQCSKQSIYKTIESKAQECFQERS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide
formula_weight	415.5 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1620

▶

6. Citations (1)

▶

length_a	61.380 Å
length_b	126.270 Å
length_c	81.270 Å
angle_alpha	90.00 °
angle_beta	107.41 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	12.000 Å
r_factor	—
r_work	0.1800
r_free	0.2700

fit	/app/data/saxs_computation/bk/1bkc/1bkc.fit
pddf	/app/data/pr_computation/bk/1bkc/1bkc.pr.out
profile	/app/data/saxs_computation/bk/1bkc/1bkc.dat

CATALYTIC DOMAIN OF TNF-ALPHA CONVERTING ENZYME (TACE)

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)