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9r0k

Structure of the human heterotetrameric cis-prenyltransferase complex in its apo form

Method: X-RAY DIFFRACTION D_max: 82.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r0k
deposition_date	2025-04-24
title	Structure of the human heterotetrameric cis-prenyltransferase complex in its apo form
keywords	cis-prenyltransferase, dolichol, 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	25.39 Å
rg_electron	24.34 Å
i0	44592200.00
molecular_weight	48385.0 kDa
excluded_volume	58911 Å³
envelope_volume	78343 Å³
shell_volume	27220 Å³
envelope_diameter	85.3 Å
shell_rg	31.00 Å
envelope_rg	24.64 Å
shape_rg	24.36 Å
total_rg	25.02 Å
total_atoms	3427
n_residues	514
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	82.3 Å
rg_real	25.32 Å
rg_real_error	0.52 Å
i0_real	4.4590e+07
i0_real_error	6.1020e+05
rg_reciprocal	25.35 Å
i0_reciprocal	44590000.0000
total_estimate	0.8987
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.0 Å
skewness	0.257
kurtosis	-0.400
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	7347000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Dehydrodolichyl diphosphate synthase complex subunit DHDDS
formula_weight	39202.0 kDa
ec_number	2.5.1.87
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3434

GSGSGSGMSWIKEGELSLWERFCANIIKAGPMPKHIAFIMDGNRRYAKKCQVERQEGHSQGFNKLAETLRWCLNLGILEVTVYAFSIENFKRSKSEVDGLMDLARQKFSRLMEEKEKLQKHGVCIRVLGDLHLLPLDLQELIAQAVQATKNYNKCFLNVCFAYTSRHEISNAVREMAWGVEQGLLDPSDISESLLDKCLYTNRSPHPDILIRTSGEVRLSDFLLWQTSHSCLVFQPVLWPEYTFWNLFEAILQFQMNHSVLQKARDMYAEERKRQQLERDQATVTEQLLREGLQASGDAQLRRTRLHKLSARREERVQGFLQALELKRADWLARLGTASA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Dehydrodolichyl diphosphate synthase complex subunit NUS1
formula_weight	24789.2 kDa
ec_number	2.5.1.87
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQLVAQKQKRPTDLDVDTLASLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIVSLPSHLNISYEDFFSALRQYAACEQRLGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	183.346 Å
length_b	183.346 Å
length_c	112.356 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	2.890 Å
resolution_low	41.013 Å
r_factor	0.2668
r_work	0.2649
r_free	0.3021

fit	/app/data/saxs_computation/r0/9r0k/9r0k.fit
pddf	/app/data/pr_computation/r0/9r0k/9r0k.pr.out
profile	/app/data/saxs_computation/r0/9r0k/9r0k.dat

Structure of the human heterotetrameric cis-prenyltransferase complex in its apo form

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)