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9r08

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249A in complex with magnesium, FsPP and IPP

Method: X-RAY DIFFRACTION D_max: 85.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r08
deposition_date	2025-04-24
title	Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249A in complex with magnesium, FsPP and IPP
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	25.80 Å
rg_electron	24.73 Å
i0	57230200.00
molecular_weight	58121.0 kDa
excluded_volume	72363 Å³
envelope_volume	87474 Å³
shell_volume	29481 Å³
envelope_diameter	89.2 Å
shell_rg	31.83 Å
envelope_rg	25.19 Å
shape_rg	24.75 Å
total_rg	25.42 Å
total_atoms	4087
n_residues	529
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	85.7 Å
rg_real	25.73 Å
rg_real_error	0.57 Å
i0_real	5.7230e+07
i0_real_error	8.2550e+05
rg_reciprocal	25.76 Å
i0_reciprocal	57230000.0000
total_estimate	0.8893
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.267
kurtosis	-0.383
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	7937000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	4197

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	24773.2 kDa
ec_number	2.5.1.87
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQLVAQKQKRPTDLDVDTLASLLSSNGCPDPDLVLKFGPVDATLGFLPWHIRLTEIVSLPSHLNISYEDFFSALRQYAACEQRLGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
formula_weight	246.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE
formula_weight	398.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	99

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6. Citations (1)

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length_a	184.399 Å
length_b	184.399 Å
length_c	112.575 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	2.400 Å
resolution_low	46.100 Å
r_factor	0.1980
r_work	0.1959
r_free	0.2408

fit	/app/data/saxs_computation/r0/9r08/9r08.fit
pddf	/app/data/pr_computation/r0/9r08/9r08.pr.out
profile	/app/data/saxs_computation/r0/9r08/9r08.dat

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249A in complex with magnesium, FsPP and IPP

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)