SAXSdb — 1e4e

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1. Structure Basics

entry_id	1e4e
deposition_date	2000-07-03
title	D-alanyl-D-lacate ligase
keywords	LIGASE, CELL WALL, ANTIBIOTIC RESISTANCE, MEMBRANE, PEPTIDOGLYCAN SYNTHESIS; 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	26.59 Å
rg_electron	25.55 Å
i0	99708300.00
molecular_weight	77188.0 kDa
excluded_volume	96194 Å³
envelope_volume	112370 Å³
shell_volume	35106 Å³
envelope_diameter	83.0 Å
shell_rg	34.23 Å
envelope_rg	25.84 Å
shape_rg	25.57 Å
total_rg	26.37 Å
total_atoms	5395
n_residues	681
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	81.7 Å
rg_real	26.44 Å
rg_real_error	0.39 Å
i0_real	9.9710e+07
i0_real_error	1.4140e+06
rg_reciprocal	26.49 Å
i0_reciprocal	99710000.0000
total_estimate	0.9098
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.7 Å
skewness	0.156
kurtosis	-0.565
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	46060000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
formula_weight	37575.0 kDa
ec_number	6.1.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5750

MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLALKG

Source

organism	ENTEROCOCCUS FAECIUM
ncbi_taxonomy_id	1352
host_organism	ESCHERICHIA COLI

Entity 2 polymer

description	VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
formula_weight	37618.1 kDa
ec_number	6.1.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQDRGRIVLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLALKG

Source

organism	ENTEROCOCCUS FAECIUM
ncbi_taxonomy_id	1352
host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

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

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	14

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	355

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6. Citations (1)

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length_a	123.204 Å
length_b	225.359 Å
length_c	72.439 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.500 Å
resolution_low	15.000 Å
r_factor	—
r_work	0.1830
r_free	0.2570

fit	/app/data/saxs_computation/e4/1e4e/1e4e.fit
pddf	/app/data/pr_computation/e4/1e4e/1e4e.pr.out
profile	/app/data/saxs_computation/e4/1e4e/1e4e.dat

D-alanyl-D-lacate 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

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)