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9s2t

Carbamoyl transferase NovN involved in Novobiocin biosynthesis

Method: X-RAY DIFFRACTION D_max: 81.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s2t
deposition_date	2025-07-22
last_revision	2025-07-30
title	Carbamoyl transferase NovN involved in Novobiocin biosynthesis
keywords	carbamoylation, transferase, homodimer, novobiocin; 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	26.09 Å
rg_electron	25.10 Å
i0	93195100.00
molecular_weight	74182.0 kDa
excluded_volume	92127 Å³
envelope_volume	110810 Å³
shell_volume	35343 Å³
envelope_diameter	84.8 Å
shell_rg	33.47 Å
envelope_rg	25.39 Å
shape_rg	25.10 Å
total_rg	25.94 Å
total_atoms	5225
n_residues	669
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	81.3 Å
rg_real	25.94 Å
rg_real_error	0.43 Å
i0_real	9.3200e+07
i0_real_error	1.1900e+06
rg_reciprocal	25.99 Å
i0_reciprocal	93200000.0000
total_estimate	0.8937
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.3 Å
skewness	0.166
kurtosis	-0.417
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	39580000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Decarbamoylnovobiocin carbamoyltransferase
formula_weight	75773.4 kDa
ec_number	2.1.3.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5747

MLILGLNGNVSAAGADVVPNLNELYMHDAAATLVRDGVLVAAVEEERLNRIKKTTKFPSNAIRECLAAAGAKPADVDAIAYYFPEDFFDDIFQQLYTEHPSVPTRYSREMILERLRVDLGWAAPPDILHYVPHHLAHAMSTYYRSGMREALVVVMDGAGERNCTTIYRSDGAELFEIASYPVPKSLGMFYLYGTRHLGYGFGDEYKVMGLAPYGDPSTYRDVFSTLYSLGPNGTYELIPRGGVVFRMTTILREHGLQPRRRGEPFTQAHMDFAASVQETTEQIAMHVIGYWARSTGLRNLAFGGGVAHNSTLNGRILTSGLFDEVFVHPASHDAGSSEGAALVVARERGERVWPLPRLTNASLGPDLGDVDSLERTLKSWSPLVDVERPDDIVEATAHLLAAGEAIGWAHGRSEFGPRALGNRSILADARPKENQTRINAMVKKRESFRPFAPVVTAEAAGDYFDLPETVGHHDFMSFVVQVRADRRELLGAVTHVDGSARVQVVTEETNPRFHRLVTRFGELTGTPVLLNTSFNNHAEPIVQSVDDVLTSYLTTSLDVLVIEDFVVRRRTELPLALEDFTIGFRPVTRLVRRLADVSAGRPGAPEVSHEIYLDHTSGPRATISAAMYELLTHADGVTPLGSLGIELTGELLTELYDLWQGRFVTVAPVGDGAGSAPLEHHHHHHHH

Source

organism	Streptomyces niveus
ncbi_taxonomy_id	193462
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	434

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6. Citations (2)

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length_a	108.500 Å
length_b	113.260 Å
length_c	166.710 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	2.240 Å
resolution_low	39.173 Å
r_factor	—
r_work	0.1599
r_free	0.2000

fit	/app/data/saxs_computation/s2/9s2t/9s2t.fit
pddf	/app/data/pr_computation/s2/9s2t/9s2t.pr.out
profile	/app/data/saxs_computation/s2/9s2t/9s2t.dat

Carbamoyl transferase NovN involved in Novobiocin biosynthesis

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