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9yz5

human FicD bound with farnesyl pyrophosphate

Method: X-RAY DIFFRACTION D_max: 96.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yz5
deposition_date	2025-10-30
title	human FicD bound with farnesyl pyrophosphate
keywords	AMPylation, 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	30.61 Å
rg_electron	29.76 Å
i0	92114300.00
molecular_weight	76444.0 kDa
excluded_volume	96090 Å³
envelope_volume	125290 Å³
shell_volume	35164 Å³
envelope_diameter	96.8 Å
shell_rg	37.10 Å
envelope_rg	29.02 Å
shape_rg	29.77 Å
total_rg	30.44 Å
total_atoms	5378
n_residues	658
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	96.4 Å
rg_real	30.52 Å
rg_real_error	0.65 Å
i0_real	9.2110e+07
i0_real_error	1.3470e+06
rg_reciprocal	30.56 Å
i0_reciprocal	92120000.0000
total_estimate	0.9086
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	94.5 Å
skewness	0.176
kurtosis	-0.563
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	12500000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein adenylyltransferase FICD
formula_weight	37977.5 kDa
ec_number	2.7.7.108,3.1.4.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5462

SEARAALNQALEMKRQGKREKAQKLFMHALKMDPDFVDALTEFGIFSEEDKDIIQADYLYTRALTISPYHEKALVNRDRTLPLVEEIDQRYFSIIDSKVKKVMSIPKGNSALRRVMEETYYHHIYHTVAIGGNTLTLSEIRHILETRYAVPGKSLEEQNEVIGMHAAMKYINTTLVSRIGSVTISDVLEIHRRVLGYVDPVEAGRFRTTQVLVGHHIPPHPQDVEKQMQEFVQWLNSEEAMNLHPVEFAALAHYKLVYIHPFIDGNGRTSRLLMNLILMQAGYPPITIRKEQRSDYYHVLEAANEGDVRPFIRFIAKCTETTLDTLLFAT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	FARNESYL DIPHOSPHATE
formula_weight	382.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	84

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6. Citations (1)

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length_a	71.021 Å
length_b	76.983 Å
length_c	91.325 Å
angle_alpha	90.00 °
angle_beta	107.20 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.580 Å
resolution_low	48.940 Å
r_factor	0.2374
r_work	0.2335
r_free	0.2904

fit	/app/data/saxs_computation/yz/9yz5/9yz5.fit
pddf	/app/data/pr_computation/yz/9yz5/9yz5.pr.out
profile	/app/data/saxs_computation/yz/9yz5/9yz5.dat

human FicD bound with farnesyl pyrophosphate

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