SAXSdb — 9skm

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1. Structure Basics

entry_id	9skm
deposition_date	2025-09-02
title	Biocatalytic Regioselective C-Formylation of Resorcinol Derivatives (CsATase C88S)
keywords	C-formylation of phenolic substrates, 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	44.95 Å
rg_electron	44.43 Å
i0	2265590000.00
molecular_weight	388620.0 kDa
excluded_volume	482900 Å³
envelope_volume	572210 Å³
shell_volume	100950 Å³
envelope_diameter	148.2 Å
shell_rg	53.31 Å
envelope_rg	44.35 Å
shape_rg	44.40 Å
total_rg	44.83 Å
total_atoms	53967
n_residues	3593
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	147.2 Å
rg_real	44.80 Å
rg_real_error	0.85 Å
i0_real	2.2660e+09
i0_real_error	3.8320e+07
rg_reciprocal	44.94 Å
i0_reciprocal	2266000000.0000
total_estimate	0.8748
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.7 Å
skewness	0.284
kurtosis	-0.323
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0001
highest_alpha	864500000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.821

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	2,4-diacetylphloroglucinol biosynthesis protein
formula_weight	38165.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	56670

MKKIGIVSYGSSIPTCRLKINDVIDVWKNTDLDLVKNHLGVCERAVLQPDEDVITLGVQAAQRALEHAGSPTLDALHLGTCTNPYDSRSSAAIILEMLGQGYDMYCADVQFSGKSGTSALQISQALVASGMAGHALAIAADAINRHTAPGDLTESYAGAGAAAMLVGSENLIAEIDGTFSCAADIADNIRPQGERYIRSGMGLGSDKNSIGLEDQTRRAAEGLMGKLKTSASDFDYVVFQQNVVSTPRSLGKLLGFTAEQLEPALFADTIGDTGAASPLLGLIQVLDQAKPGDRILLVSYGFGAGSDAIALTVTDNIAAHQQRATTLKTQLGQKQYVDYGTAIKYEFKYLRPDYALTAYL

Source

organism	Chromobacterium sphagni
ncbi_taxonomy_id	1903179
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	2,4-diacetylphloroglucinol biosynthesis protein
formula_weight	16517.4 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,F,G,H

MSLYPEHIHRMTTASMLREWREHGGKYRLEGSRCQECEAIFFPRRSVCGACNSLKIEPYGCKRHGTIVALSRAENPILAGMGYGEAVPRHMVMLRLDDGIGIASEVVDILDPAKLKIGARVKMVIRKHVRESNLAWQYAYKFVLE

Source

organism	Chromobacterium sphagni
ncbi_taxonomy_id	1903179
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	2,4-diacetylphloroglucinol biosynthesis protein
formula_weight	42719.9 kDa
mutation	C88S
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	I,J,K,L

MSARRVAIVSAAYTPKPGSSRVRQTFKEMIVESAYKAIRDAKMHPREIQGVAYGYHGEGISEYGGLGPTISDALGISPAPTFITSSNSTSSSVSFQMGHQMVASGEYDIVLCGGFEKMTDHFNYAEYIGSSTECEYDYFLGISHTDAFALATSEYFHKYGYAGREADVLAHFGRQMRIYAQNTPSATRYGQAIPSLEALKASEAHGSMLAWGEASGCAILVAEHLAHKYTDKPVFIKGCAYTGVSHYFGTRYHNPTLQYPGLPQDVGMALSANSIACAEMAYKKAGITAKDIDVAQVYDLLGAGLIQMESMGICQPGQAGHFVMEGGIALDGQVPLNTDGGNIGRGHASGCDGILHITELFRQLRGEADNQVKNARIAVSQNLGGYAAHNSVIVLTNE

Source

organism	Chromobacterium sphagni
ncbi_taxonomy_id	1903179
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	11

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	9

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2612

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6. Citations (1)

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length_a	93.733 Å
length_b	184.359 Å
length_c	120.782 Å
angle_alpha	90.00 °
angle_beta	103.66 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.870 Å
resolution_low	64.920 Å
r_factor	0.1668
r_work	0.1654
r_free	0.1934

fit	/app/data/saxs_computation/sk/9skm/9skm.fit
pddf	/app/data/pr_computation/sk/9skm/9skm.pr.out
profile	/app/data/saxs_computation/sk/9skm/9skm.dat

Biocatalytic Regioselective C-Formylation of Resorcinol Derivatives (CsATase C88S)

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)