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1ehi

D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES

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	1ehi
deposition_date	2000-02-21
title	D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES
keywords	ATP-binding. Grasp motif for ATP., LIGASE; 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	26.79 Å
rg_electron	25.53 Å
i0	99779600.00
molecular_weight	78966.0 kDa
excluded_volume	99032 Å³
envelope_volume	117120 Å³
shell_volume	36732 Å³
envelope_diameter	79.0 Å
shell_rg	34.32 Å
envelope_rg	25.59 Å
shape_rg	25.52 Å
total_rg	26.48 Å
total_atoms	5576
n_residues	707
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	26.61 Å
rg_real_error	0.29 Å
i0_real	9.9780e+07
i0_real_error	1.2470e+06
rg_reciprocal	26.67 Å
i0_reciprocal	99780000.0000
total_estimate	0.9099
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.2 Å
skewness	0.120
kurtosis	-0.534
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	32240000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.914

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	D-ALANINE:D-LACTATE LIGASE
formula_weight	41866.9 kDa
ec_number	6.3.2.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5789

MTKKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSKKILALEDEQPIVDAFMKTVDASDPLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGHAVSFDKALTKELLTVNGIRNTKYIVVDPESANNWSWDKIVAELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSFQYDYKVLIEEAVNGARELEVGVIGNDQPLVSEIGAHTVPNQGSGDGWYDYNNKFVDNSAVHFQIPAQLSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNVPYLGEPNTLPGFTNMSLFKRLWDYSDINNAKLVDMLIDYGFEDFAQNKKLSYSFVSLGEEKIGKFN

Source

organism	Leuconostoc mesenteroides
ncbi_taxonomy_id	1245
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 non-polymer

description	1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
formula_weight	275.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	213

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6. Citations (3)

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length_a	118.200 Å
length_b	90.800 Å
length_c	82.100 Å
angle_alpha	90.00 °
angle_beta	92.10 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.380 Å
resolution_low	100.000 Å
r_factor	0.1840
r_work	0.1840
r_free	0.2570

fit	/app/data/saxs_computation/eh/1ehi/1ehi.fit
pddf	/app/data/pr_computation/eh/1ehi/1ehi.pr.out
profile	/app/data/saxs_computation/eh/1ehi/1ehi.dat