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9s1q

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

Method: X-RAY DIFFRACTION D_max: 111.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1q
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
keywords	pyridoxal phosphate Crystal structure DABA aminotransferase, 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	37.12 Å
rg_electron	36.56 Å
i0	502673000.00
molecular_weight	182950.0 kDa
excluded_volume	228720 Å³
envelope_volume	273270 Å³
shell_volume	59817 Å³
envelope_diameter	114.1 Å
shell_rg	44.71 Å
envelope_rg	36.51 Å
shape_rg	36.57 Å
total_rg	37.00 Å
total_atoms	12846
n_residues	1672
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	111.7 Å
rg_real	37.03 Å
rg_real_error	0.53 Å
i0_real	5.0270e+08
i0_real_error	6.6720e+06
rg_reciprocal	37.09 Å
i0_reciprocal	502700000.0000
total_estimate	0.8819
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.0 Å
skewness	0.226
kurtosis	-0.668
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	378400000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.548

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Diaminobutyrate-2-oxoglutarate transaminase
formula_weight	46704.9 kDa
ec_number	2.6.1.76
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13487

MEIFKSTESEVRVYSRAFPVIFNRAKNAHLYTEDGKQYLDFLAGAGSLNYGHNNDTLKKALLEYIESDGVSQGLDMFTTAKQGFMEAYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKVKGRTGIISFTNGFHGVTMGAVAATGNKHHRGGVGAPLSNVDFMFYDGYLGEDVDSLAIMDKLLSDGSSGVEVPAAVIVEAVQGEGGLNAARAEWLKGLEALCKKHDMLLILDDIQAGNGRTGEFFSFEFAGITPDIVTVSKSLSGYGLPMALVLFKPELDIWSSGEHNGTFRGNNMAFVTARAAIETYWKDDSFANEVKEKTQVLGDALQAICDKYPGEFKMKGRGLMRGIEATNADITGPVTKRAFEHGLIIETSGPNDEVIKCLMPLTTSKDDLKLGAELLAKSVDEIMQESMSKASHHHHHH

Source

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

Entity 2 non-polymer

description	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
formula_weight	248.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	641

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6. Citations (1)

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length_a	80.648 Å
length_b	99.332 Å
length_c	112.698 Å
angle_alpha	90.00 °
angle_beta	104.82 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	40.130 Å
r_factor	0.1675
r_work	0.1654
r_free	0.2082

fit	/app/data/saxs_computation/s1/9s1q/9s1q.fit
pddf	/app/data/pr_computation/s1/9s1q/9s1q.pr.out
profile	/app/data/saxs_computation/s1/9s1q/9s1q.dat

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

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