← Back to search

9tb4

SAM-dependent C6-FPP methytransferase from Streptomyces varsoviensis in complex with SAH and FPP

Method: X-RAY DIFFRACTION D_max: 175.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9tb4
deposition_date	2025-11-19
title	SAM-dependent C6-FPP methytransferase from Streptomyces varsoviensis in complex with SAH and FPP
keywords	Methyltransferase, Isoprenoid Modification, FPP, Natural Product Biosynthesis, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	54.08 Å
rg_electron	53.72 Å
i0	2036200000.00
molecular_weight	372900.0 kDa
excluded_volume	464540 Å³
envelope_volume	687160 Å³
shell_volume	106440 Å³
envelope_diameter	182.0 Å
shell_rg	57.46 Å
envelope_rg	51.99 Å
shape_rg	53.71 Å
total_rg	53.87 Å
total_atoms	26308
n_residues	3292
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

▼

3. P(r) Analysis (GNOM)

dmax	175.8 Å
rg_real	53.86 Å
rg_real_error	1.49 Å
i0_real	2.0360e+09
i0_real_error	3.5170e+07
rg_reciprocal	54.25 Å
i0_reciprocal	2037000000.0000
total_estimate	0.8900
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.7 Å
skewness	0.110
kurtosis	-0.505
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	88730000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.893

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (9)

Entity 1 polymer

description	C6-FPP methytransferase
formula_weight	33413.6 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	27128

SDNSIVAEATADRGTVIGEAKVPSYYSRKTTDILHKYGPGPRVHFHMGLFDAGAAPNTTVAQRVLKDRLLVSQETAIQHADRAWNVAADRPAALLDIGCGLGGGSLYWAQEHGCAVTAMTVAAQHVPLVAEFAELAGVGELVTPVLADIHDLREERAYGAAVAFESSGYMDRERLFGVVAKALEPGGWFGIQEHFLCRPEWTRFIDGYYKTRLGTLAEYIAAANAAGFELEQDEDITDRAAEFWVQSMAWTTAELDMAKRSGRPSPIAVERLTESALTHGKLFRIWRDHAVETRQLLFRLQDR

Source

organism	Streptomyces varsoviensis
ncbi_taxonomy_id	67373
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FARNESYL DIPHOSPHATE
formula_weight	382.3 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
formula_weight	370.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 8 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	820

▶

6. Citations (1)

▶

length_a	130.560 Å
length_b	133.330 Å
length_c	231.420 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	48

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.200 Å
resolution_low	30.000 Å
r_factor	0.2103
r_work	0.2089
r_free	0.2374

fit	/app/data/saxs_computation/tb/9tb4/9tb4.fit
pddf	/app/data/pr_computation/tb/9tb4/9tb4.pr.out
profile	/app/data/saxs_computation/tb/9tb4/9tb4.dat