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9v4i

Prenyltransferase Ord1 D219A

Method: X-RAY DIFFRACTION D_max: 116.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v4i
deposition_date	2025-05-23
title	Prenyltransferase Ord1 D219A
keywords	Transferase, Prenyltransferase; 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	35.10 Å
rg_electron	34.47 Å
i0	239354000.00
molecular_weight	122160.0 kDa
excluded_volume	152240 Å³
envelope_volume	203010 Å³
shell_volume	49303 Å³
envelope_diameter	121.0 Å
shell_rg	40.79 Å
envelope_rg	34.21 Å
shape_rg	34.49 Å
total_rg	34.88 Å
total_atoms	8568
n_residues	1147
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	116.2 Å
rg_real	36.13 Å
rg_real_error	0.39 Å
i0_real	2.3790e+08
i0_real_error	3.1950e+06
rg_reciprocal	35.09 Å
i0_reciprocal	239400000.0000
total_estimate	0.6913
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	43.9 Å
skewness	0.439
kurtosis	-0.118
angular_range	— – 0.2250 Å⁻¹
current_alpha	2.6710
highest_alpha	33200000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 0.906; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.625

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	prenyltransferase
formula_weight	36151.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8576

MTDIDVPQVADPEVAAMVRAEVEGRWPLGVSGLDEVVRYGLVPFGKMMGPWLLIRSALAVGGDIATALPAAVALECVQVGAMMHDDIIDCDAQRRSKPAAHTVFGEPTAIVGGDGLFFHGFAALSECREAGAPAERVAQAFTVLSRAGLRIGSAALREIRMSREICSVQDYLDMIADKSGALLWMACGVGGTLGGADEAALKALSQYSDQLGIAYQIRADLMAYDGTRAGKPNISDVRNGRPTLPVLLAHERAPREQQLRIERLLADTAAPAAERYKAMADLVGAYDGAQAAREVSHRHVQLATRALQTLPPSPHRDALEDLTVPGRLVLEHHHHHH

Source

organism	Streptomyces sp. KS84
ncbi_taxonomy_id	746563
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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length_a	58.879 Å
length_b	72.425 Å
length_c	83.774 Å
angle_alpha	93.45 °
angle_beta	110.50 °
angle_gamma	90.08 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.800 Å
resolution_low	44.350 Å
r_factor	0.2307
r_work	0.2240
r_free	0.2539

fit	/app/data/saxs_computation/v4/9v4i/9v4i.fit
pddf	/app/data/pr_computation/v4/9v4i/9v4i.pr.out
profile	/app/data/saxs_computation/v4/9v4i/9v4i.dat

Prenyltransferase Ord1 D219A

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