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1e0d

UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase

Method: X-RAY DIFFRACTION D_max: 77.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e0d
deposition_date	2000-03-24
title	UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase
keywords	LIGASE, PEPTIDOGLYCAN SYNTHESIS, MURD, ADP-FORMING ENZYME; 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	25.06 Å
rg_electron	24.00 Å
i0	36470500.00
molecular_weight	45909.0 kDa
excluded_volume	57223 Å³
envelope_volume	69103 Å³
shell_volume	24299 Å³
envelope_diameter	78.9 Å
shell_rg	30.85 Å
envelope_rg	23.80 Å
shape_rg	24.01 Å
total_rg	24.75 Å
total_atoms	3220
n_residues	429
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	77.7 Å
rg_real	25.04 Å
rg_real_error	0.43 Å
i0_real	3.6470e+07
i0_real_error	4.9490e+05
rg_reciprocal	25.05 Å
i0_reciprocal	36470000.0000
total_estimate	0.9098
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.270
kurtosis	-0.551
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	9006000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
formula_weight	46889.2 kDa
ec_number	6.3.2.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3449

ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG

Source

organism	ESCHERICHIA COLI
ncbi_taxonomy_id	562
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	229

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6. Citations (1)

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length_a	69.160 Å
length_b	69.160 Å
length_c	196.710 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.400 Å
resolution_low	20.000 Å
r_factor	0.2130
r_work	0.2130
r_free	0.2620

fit	/app/data/saxs_computation/e0/1e0d/1e0d.fit
pddf	/app/data/pr_computation/e0/1e0d/1e0d.pr.out
profile	/app/data/saxs_computation/e0/1e0d/1e0d.dat

UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase

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