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1dak

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE

Method: X-RAY DIFFRACTION D_max: 57.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dak
deposition_date	1998-03-31
title	DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE
keywords	PHOSHPORYL TRANSFER, BIOTIN BIOSYNTHESIS, LIGASE, KINETIC CRYSTALLOGRAPHY; LIGASE
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	17.79 Å
rg_electron	16.71 Å
i0	11475600.00
molecular_weight	24887.0 kDa
excluded_volume	31009 Å³
envelope_volume	34694 Å³
shell_volume	17180 Å³
envelope_diameter	57.7 Å
shell_rg	23.10 Å
envelope_rg	17.11 Å
shape_rg	16.70 Å
total_rg	17.73 Å
total_atoms	1746
n_residues	224
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	57.3 Å
rg_real	17.67 Å
rg_real_error	0.37 Å
i0_real	1.1480e+07
i0_real_error	1.4220e+05
rg_reciprocal	17.69 Å
i0_reciprocal	11480000.0000
total_estimate	0.8057
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.2 Å
skewness	0.175
kurtosis	-0.339
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	2486000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DETHIOBIOTIN SYNTHETASE
formula_weight	24028.3 kDa
ec_number	6.3.3.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1962

SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID
formula_weight	312.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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6. Citations (1)

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length_a	72.680 Å
length_b	48.190 Å
length_c	61.070 Å
angle_alpha	90.00 °
angle_beta	106.58 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.600 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1840
r_free	0.2100

fit	/app/data/saxs_computation/da/1dak/1dak.fit
pddf	/app/data/pr_computation/da/1dak/1dak.pr.out
profile	/app/data/saxs_computation/da/1dak/1dak.dat