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9vl0

CYP105A1 complexed with simvastatin (cryogenic data collection)

Method: X-RAY DIFFRACTION D_max: 72.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vl0
deposition_date	2025-06-24
last_revision	2025-10-08
title	CYP105A1 complexed with simvastatin (cryogenic data collection)
keywords	P450, CYP105A1, statin, simvastatin, OXIDOREDUCTASE; OXIDOREDUCTASE
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	22.43 Å
rg_electron	21.13 Å
i0	34777300.00
molecular_weight	45228.0 kDa
excluded_volume	56513 Å³
envelope_volume	66134 Å³
shell_volume	25516 Å³
envelope_diameter	75.9 Å
shell_rg	28.58 Å
envelope_rg	21.60 Å
shape_rg	21.14 Å
total_rg	21.95 Å
total_atoms	3184
n_residues	406
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	72.4 Å
rg_real	22.32 Å
rg_real_error	0.31 Å
i0_real	3.4780e+07
i0_real_error	4.1030e+05
rg_reciprocal	22.35 Å
i0_reciprocal	34780000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.211
kurtosis	-0.370
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	7428000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Vitamin D3 dihydroxylase
formula_weight	44991.7 kDa
ec_number	1.14.15.-
mutation	R84A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3573

MTDTATTPQTTDAPAFPSNRSCPYQLPDGYAQLRDTPGPLHRVTLYDGRQAWVVTKHEAARKLLGDPRLSSNRTDDNFPATSPAFEAVRESPQAFIGLDPPEHGTRRRMTISEFTVKRIKGMRPEVEEVVHGFLDEMLAAGPTADLVSQFALPVPSMVICRLLGVPYADHEFFQDASKRLVQSTDAQSALTARNDLAGYLDGLITQFQTEPGAGLVGALVADQLANGEIDREELISTAMLLLIAGHETTASMTSLSVITLLDHPEQYAALRADRSLVPGAVEELLRYLAIADIAGGRVATADIEVEGQLIRAGEGVIVVNSIANRDGTVYEDPDALDIHRSARHHLAFGFGVHQCLGQNLARLELEVILNALMDRVPTLRLAVPVEQLVLRPGTTIQGVNELPVTWHHHHHH

Source

organism	Streptomyces griseolus
ncbi_taxonomy_id	1909
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	291

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6. Citations (1)

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length_a	52.000 Å
length_b	53.202 Å
length_c	138.801 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.600 Å
resolution_low	34.700 Å
r_factor	0.1559
r_work	0.1535
r_free	0.2021

fit	/app/data/saxs_computation/vl/9vl0/9vl0.fit
pddf	/app/data/pr_computation/vl/9vl0/9vl0.pr.out
profile	/app/data/saxs_computation/vl/9vl0/9vl0.dat