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9s1p

Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1 -Mutant K264A

Method: X-RAY DIFFRACTION D_max: 70.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1p
deposition_date	2025-07-18
last_revision	2026-02-18
title	Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1 -Mutant K264A
keywords	pyridoxal phosphate Crystal structure DABA aminotransferase mutant, 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	22.65 Å
rg_electron	21.53 Å
i0	35896200.00
molecular_weight	45877.0 kDa
excluded_volume	57275 Å³
envelope_volume	68031 Å³
shell_volume	25769 Å³
envelope_diameter	71.5 Å
shell_rg	28.85 Å
envelope_rg	21.75 Å
shape_rg	21.51 Å
total_rg	22.49 Å
total_atoms	3219
n_residues	419
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	70.8 Å
rg_real	22.53 Å
rg_real_error	0.34 Å
i0_real	3.5900e+07
i0_real_error	4.4680e+05
rg_reciprocal	22.56 Å
i0_reciprocal	35900000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.161
kurtosis	-0.449
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	6087000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Diaminobutyrate-2-oxoglutarate transaminase
formula_weight	46646.8 kDa
ec_number	2.6.1.76
mutation	K264A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	3769

MEIFKSTESEVRVYSRAFPVIFNRAKNAHLYTEDGKQYLDFLAGAGSLNYGHNNDTLKKALLEYIESDGVSQGLDMFTTAKQGFMEAYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKVKGRTGIISFTNGFHGVTMGAVAATGNKHHRGGVGAPLSNVDFMFYDGYLGEDVDSLAIMDKLLSDGSSGVEVPAAVIVEAVQGEGGLNAARAEWLKGLEALCKKHDMLLILDDIQAGNGRTGEFFSFEFAGITPDIVTVSASLSGYGLPMALVLFKPELDIWSSGEHNGTFRGNNMAFVTARAAIETYWKDDSFANEVKEKTQVLGDALQAICDKYPGEFKMKGRGLMRGIEATNADITGPVTKRAFEHGLIIETSGPNDEVIKCLMPLTTSKDDLKLGAELLAKSVDEIMQESMSKASHHHHHH

Source

organism	Marinobacter sp. CK-1
ncbi_taxonomy_id	1379940
host_organism	Escherichia coli

Entity 2 non-polymer

description	PYRIDOXAL-5'-PHOSPHATE
formula_weight	247.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	402

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6. Citations (1)

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length_a	67.027 Å
length_b	79.893 Å
length_c	180.161 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.550 Å
resolution_low	48.050 Å
r_factor	0.1393
r_work	0.1381
r_free	0.1633

fit	/app/data/saxs_computation/s1/9s1p/9s1p.fit
pddf	/app/data/pr_computation/s1/9s1p/9s1p.pr.out
profile	/app/data/saxs_computation/s1/9s1p/9s1p.dat