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1es3

C98A mutant of streptomyces K15 DD-transpeptidase

Method: X-RAY DIFFRACTION D_max: 63.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1es3
deposition_date	2000-04-07
title	C98A mutant of streptomyces K15 DD-transpeptidase
keywords	PENICILLIN-BINDING, DD-TRANSPEPTIDASE, SERINE PEPTIDASE, BETA-LACTAMASE, HYDROLASE CARBOXYPEPTIDASE, HYDROLASE; HYDROLASE
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	18.66 Å
rg_electron	17.69 Å
i0	13383600.00
molecular_weight	27283.0 kDa
excluded_volume	34171 Å³
envelope_volume	37930 Å³
shell_volume	17994 Å³
envelope_diameter	63.7 Å
shell_rg	23.85 Å
envelope_rg	17.95 Å
shape_rg	17.67 Å
total_rg	18.63 Å
total_atoms	1913
n_residues	260
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	63.2 Å
rg_real	18.58 Å
rg_real_error	0.45 Å
i0_real	1.3380e+07
i0_real_error	1.8770e+05
rg_reciprocal	18.60 Å
i0_reciprocal	13380000.0000
total_estimate	0.8707
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.5 Å
skewness	0.265
kurtosis	-0.271
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	3313000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DD-TRANSPEPTIDASE
formula_weight	27476.3 kDa
ec_number	3.4.16.4
mutation	C98A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2043

VTKPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANNASQAHLIVGDKVTVRQLLYGLMLPSGADAAYALADKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVLASTSIPARESDATKIMNYGFAL

Source

organism	Streptomyces sp.
ncbi_taxonomy_id	1958
host_organism	Streptomyces lividans TK24

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	130

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6. Citations (3)

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length_a	46.305 Å
length_b	54.090 Å
length_c	108.769 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.200 Å
resolution_low	10.000 Å
r_factor	0.1740
r_work	0.1740
r_free	0.2450

fit	/app/data/saxs_computation/es/1es3/1es3.fit
pddf	/app/data/pr_computation/es/1es3/1es3.pr.out
profile	/app/data/saxs_computation/es/1es3/1es3.dat

C98A mutant of streptomyces K15 DD-transpeptidase

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