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9w5x

Crystal structure of Namat in complex with nicotinamide

Method: X-RAY DIFFRACTION D_max: 134.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w5x
deposition_date	2025-08-02
title	Crystal structure of Namat in complex with nicotinamide
keywords	Namat, NAD, Phage, bacterial immunity, immune evasion, VIRAL PROTEIN; VIRAL PROTEIN
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	41.57 Å
rg_electron	41.03 Å
i0	706655000.00
molecular_weight	223010.0 kDa
excluded_volume	280370 Å³
envelope_volume	347540 Å³
shell_volume	68734 Å³
envelope_diameter	144.0 Å
shell_rg	47.70 Å
envelope_rg	40.96 Å
shape_rg	41.00 Å
total_rg	41.45 Å
total_atoms	15713
n_residues	1941
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	134.1 Å
rg_real	41.51 Å
rg_real_error	1.01 Å
i0_real	7.0670e+08
i0_real_error	1.2350e+07
rg_reciprocal	41.57 Å
i0_reciprocal	706700000.0000
total_estimate	0.8292
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.9 Å
skewness	0.253
kurtosis	-0.536
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	303000000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Nicotinamide phosphoribosyltransferase
formula_weight	55800.1 kDa
ec_number	2.4.2.12
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16323

MTKYTYPATLLCDFYKVSHKEQYPEGTELIYSTWTPRTSRVEDIDRVVAFGFQGFIKKYLIDYFNENFFKRPKQDVVNEYKRVIKHTLQVDDPDASHIESLHELGYLPIKIKAVKEGTFIPIKVPMLTIENTIPEFFWITNYLETLMSNEIWQPTTSATLAYEYRKILDEYAMETVGNKLAVDFQGHDFSMRGMSSLESTKLSGAGHLLSFTGTDTIPAILYHEEFYNANIENELVGSSIPATEHSVMCANGQDEYVVFKKLITETYPEGFVSIVSDTWDFWNVIDTVVRKLKGDILKRDGKVVIRPDSGDPVKIICGDPEAKDELVRKGLIEVLWDIFGGNVTDKGYKVLDPHIGAIYGDAITISRCKEICKKLAAKGFASVNVVFGIGSFTYQYNTRDTFGFAMKATYTVVNGEERQIFKNPKTDDGTKKSQKGLVAVVNNGNELSLVDELDRNAYKQLSNDDILEDVFINGQLLRNQTLSEIRELLLD

Source

organism	Bacillus phage SPbetaL1
ncbi_taxonomy_id	3053435
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	NICOTINAMIDE
formula_weight	122.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	nat
entity_count	19

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	610

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6. Citations (1)

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length_a	64.061 Å
length_b	104.737 Å
length_c	119.668 Å
angle_alpha	109.31 °
angle_beta	101.55 °
angle_gamma	89.97 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.400 Å
resolution_low	38.790 Å
r_factor	0.2241
r_work	0.2233
r_free	0.2400

fit	/app/data/saxs_computation/w5/9w5x/9w5x.fit
pddf	/app/data/pr_computation/w5/9w5x/9w5x.pr.out
profile	/app/data/saxs_computation/w5/9w5x/9w5x.dat