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1dty

CRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMINOTRANSFERASE WITH PYRIDOXAL PHOSPHATE COFACTOR.

Method: X-RAY DIFFRACTION D_max: 87.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dty
deposition_date	2000-01-13
title	CRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMINOTRANSFERASE WITH PYRIDOXAL PHOSPHATE COFACTOR.
keywords	biotin biosynthesis, dapa, diaminopelargonic acid, diaminonanonoic acid, TRANSFERASE; TRANSFERASE
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	27.59 Å
rg_electron	26.33 Å
i0	147006000.00
molecular_weight	95285.0 kDa
excluded_volume	118770 Å³
envelope_volume	134850 Å³
shell_volume	40535 Å³
envelope_diameter	92.1 Å
shell_rg	35.54 Å
envelope_rg	26.63 Å
shape_rg	26.35 Å
total_rg	27.10 Å
total_atoms	6672
n_residues	858
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	87.7 Å
rg_real	27.43 Å
rg_real_error	0.47 Å
i0_real	1.4700e+08
i0_real_error	2.1430e+06
rg_reciprocal	27.48 Å
i0_reciprocal	147000000.0000
total_estimate	0.8895
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.230
kurtosis	-0.310
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	53380000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
formula_weight	47431.4 kDa
ec_number	2.6.1.62
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7006

MTTDDLAFDERHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGEITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWDAKGEARDRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISDGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFCQ

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	PYRIDOXAL-5'-PHOSPHATE
formula_weight	247.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	334

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6. Citations (1)

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length_a	58.280 Å
length_b	56.270 Å
length_c	121.930 Å
angle_alpha	90.00 °
angle_beta	96.96 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.140 Å
resolution_low	10.000 Å
r_factor	0.1960
r_work	0.1960
r_free	0.3280

fit	/app/data/saxs_computation/dt/1dty/1dty.fit
pddf	/app/data/pr_computation/dt/1dty/1dty.pr.out
profile	/app/data/saxs_computation/dt/1dty/1dty.dat