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1dj9

;CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY. ;

Method: X-RAY DIFFRACTION D_max: 67.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dj9
deposition_date	1999-12-02
title	;CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY. ;
keywords	;8-AMINO-7-OXONONANOATE SYNTHASE, BIOTIN, PYRIDOXAL-5'-PHOSPHATE, 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	22.53 Å
rg_electron	21.35 Å
i0	32081600.00
molecular_weight	41994.0 kDa
excluded_volume	52009 Å³
envelope_volume	62848 Å³
shell_volume	24258 Å³
envelope_diameter	68.1 Å
shell_rg	28.33 Å
envelope_rg	21.46 Å
shape_rg	21.36 Å
total_rg	22.17 Å
total_atoms	2951
n_residues	383
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	67.6 Å
rg_real	22.40 Å
rg_real_error	0.38 Å
i0_real	3.2080e+07
i0_real_error	4.3520e+05
rg_reciprocal	22.43 Å
i0_reciprocal	32080000.0000
total_estimate	0.9120
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.6 Å
skewness	0.090
kurtosis	-0.603
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	5774000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	8-AMINO-7-OXONONANOATE SYNTHASE
formula_weight	41539.1 kDa
ec_number	2.3.1.47
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3288

MSWQEKINAALDARGAADALRRRYPVAQGAGRWLVADDRQYLNFSSNDYLGLSHHPQIIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIAAMMAKEDRIAADRLSHASLLEAASLSPSQLRRFAHNDVTHLARLLASPCPGQQMVVTEGVFSMDGDSAPLAEIQQVTQQHNGWLMVDDAHGTGVIGEQGRGSCWLQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHLIYSTSMPPAQAQALRASLAVIRSDEGDARREKLAALITRFRAGVQDLPFTLADSCSAIQPLIVGDNSRALQLAEKLRQQGCWVTGIRPPTVPAGIARLRLTLTAAHEMQDIDRLLEVLHGNG

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 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	N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
formula_weight	418.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	337

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6. Citations (2)

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length_a	58.890 Å
length_b	58.890 Å
length_c	201.770 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 1 2
int_tables_number	151
crystal_system	—

resolution	2.000 Å
resolution_low	10.000 Å
r_factor	0.2120
r_work	0.2120
r_free	0.2780

fit	/app/data/saxs_computation/dj/1dj9/1dj9.fit
pddf	/app/data/pr_computation/dj/1dj9/1dj9.pr.out
profile	/app/data/saxs_computation/dj/1dj9/1dj9.dat

;CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY. ;

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