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9ule

Crystal structure of CYP105A1 R84A complexed with diclofenac (DIF) at room temperature

Method: X-RAY DIFFRACTION D_max: 72.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ule
deposition_date	2025-04-19
last_revision	2026-04-22
title	Crystal structure of CYP105A1 R84A complexed with diclofenac (DIF) at room temperature
keywords	P450, CYP105A1, nonsteroidal anti-inflammatory drugs, diclofenac, flufenamic acid, R84A, 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	22.31 Å
rg_electron	21.03 Å
i0	34289700.00
molecular_weight	44750.0 kDa
excluded_volume	55827 Å³
envelope_volume	65842 Å³
shell_volume	25549 Å³
envelope_diameter	78.9 Å
shell_rg	28.43 Å
envelope_rg	21.34 Å
shape_rg	21.05 Å
total_rg	21.86 Å
total_atoms	3150
n_residues	403
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	72.5 Å
rg_real	22.19 Å
rg_real_error	0.46 Å
i0_real	3.4290e+07
i0_real_error	4.6330e+05
rg_reciprocal	22.22 Å
i0_reciprocal	34290000.0000
total_estimate	0.8062
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.5 Å
skewness	0.194
kurtosis	-0.395
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	8588000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	3502

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	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
formula_weight	296.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	53.859 Å
length_b	54.039 Å
length_c	144.700 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	1.860 Å
resolution_low	36.170 Å
r_factor	0.1619
r_work	0.1596
r_free	0.2076

fit	/app/data/saxs_computation/ul/9ule/9ule.fit
pddf	/app/data/pr_computation/ul/9ule/9ule.pr.out
profile	/app/data/saxs_computation/ul/9ule/9ule.dat

Crystal structure of CYP105A1 R84A complexed with diclofenac (DIF) at room temperature

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